diff --git a/CHANGELOG.md b/CHANGELOG.md
index ae5d1b1..baefb5a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 - CI: install `wikifier[mcp]` only on Python ≥3.10 (`mcp` has no 3.8/3.9 wheels).
+- Regenerated committed `library.md` from a full `update-maps` so deleted 4.6.10 leftovers (`mcp/tools/{intel,status,workflow}.py`, `parsers/javascript/_parser.py`, `health.py`, `server_backup.py`) no longer appear in the file tree, Mermaid graph, or reverse-deps.
+- `generate_library_md` drops cache keys / reverse-deps whose source is not a file on disk (stale cache cannot resurrect ghosts).
+- File-tree captions prefer `*.wiki.md` purpose/role text; health *reasons* are audit stamps and are not copied as descriptions.
+- `session_bootstrap`: re-read `cache_backend` after ACS persist so creating an empty SQLite stub does not leave `cache_backend: "none"`. Additive `cache_empty` / `cache_files_indexed` distinguish sqlite-empty from no store.
+
+### Added
+- `tests/test_library_map_honesty.py`: fails if committed `library.md` names a path that is not a file on disk.
+
+### Changed
+- Agent Protocol **v0.6.1**: 4.6.x additive field notes (readiness tiers, `map_paths`, ACS v1.3 `agent_signal`, `needs_mark_green`, sqlite-empty vs `cache_backend: none`).
+- README / protocol language table: deep/ACS (Python, JS/TS) vs regex hint (Rust/Go/C/C++/C#/Java).
 
 ## [4.6.13] - 2026-08-27
 
diff --git a/CLAUDE.md b/CLAUDE.md
index 5a9415b..da977c8 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -6,7 +6,7 @@ This file provides guidance to Claude Code (claude.ai/code) when working with co
 
 Wikifier is a **zero-dependency, agent-to-agent codebase wiki**: it gives AI agents a token-efficient, queryable map of a codebase (health matrix, dependency graph, per-file wiki summaries) so they can look things up instead of re-reading full sources. The human layer (`index.html` dashboard) is strictly secondary — a read-only viewer of the same artifacts. It is deliberately NOT a general human documentation tool.
 
-**This repo dogfoods itself.** Wikifier runs on its own source, and you are expected to follow its agent protocol when working here (see below). The authoritative agent contract is `skills/run.md` (Agent Protocol v0.6 — package 4.6.x) — read it before substantive work.
+**This repo dogfoods itself.** Wikifier runs on its own source, and you are expected to follow its agent protocol when working here (see below). The authoritative agent contract is `skills/run.md` (Agent Protocol v0.6.1 — package 4.6.x) — read it before substantive work.
 
 **USE WIKIFIER FIRST (non-negotiable in this repo, preferred on any managed target):** At session start call `session_bootstrap` (MCP or `python -m wikifier session-bootstrap`). Prefer Core daily tools (`list_core_tools`): bootstrap, `check_changes`, `prepare_edit`, `suggest_next_actions` (json `actions[]`), `record_change`, `mark_green`. Look up via map/wiki/deps before re-reading full sources. Selective work only (🔴 / actionable 🟡). Never skip `record_change` after edits.
 
diff --git a/README.md b/README.md
index f4c5ce3..dea2438 100644
--- a/README.md
+++ b/README.md
@@ -8,17 +8,12 @@
 
 Wikifier is an **agent-to-agent** tool: it builds a living map of a project (health matrix, dependency graph, short file summaries) and agents keep that map current as they work. Humans can peek via a small dashboard; the product is the agent loop, not a general docs site or IDE.
 
-Works from small scripts to large monorepos. **Deep import/include maps** (zero-dep regex parsers):
-
-| Language | Extensions | Notes |
-|----------|------------|--------|
-| Python | `.py` | full ACS/CDIA path |
-| JavaScript / TypeScript | `.js` `.ts` `.jsx` `.tsx` | barrels (BREE), dynamic/CDIA |
-| Rust | `.rs` | `use` / `mod` / `extern crate` |
-| Go | `.go` | `import` / import blocks |
-| C / C++ | `.c` `.h` `.cpp` `.cc` `.cxx` `.hpp` `.hh` | `#include` (local + system) |
-| C# | `.cs` | `using` namespaces |
-| Java | `.java` | `import` / `import static` |
+Works from small scripts to large monorepos. Parsers are **zero-dep regex** (not cargo / `go.mod` / classpath / `-I`). Depth is two-tier:
+
+| Depth | Languages | What agents should trust |
+|-------|-----------|--------------------------|
+| **Deep / ACS** | Python (`.py`); JavaScript / TypeScript (`.js` `.ts` `.jsx` `.tsx` `.mjs` `.cjs` `.mts` `.cts`) | CDIA, BREE barrels, scored resolve, ACS work queue |
+| **Regex hint** | Rust (`.rs`); Go (`.go`); C / C++ (`.c` `.h` `.cpp` `.cc` `.cxx` `.hpp` `.hh`); C# (`.cs`); Java (`.java`) | `use` / `import` / `#include` / `using` smokes — not compiler-faithful |
 
 Health/journal still work for any monitored path. Parsers are **pragmatic regex** (not full cargo/`go.mod`/classpath/`-I` resolution). On huge monorepos, split scope deliberately:
 
@@ -62,7 +57,7 @@ Always set an explicit root for external trees: `WIKIFIER_PROJECT_ROOT=/abs/path
 
 ## Steady state (only touch what needs it)
 
-Full protocol: [`skills/run.md`](skills/run.md) (Agent Protocol v0.6 — package **4.6.x**).
+Full protocol: [`skills/run.md`](skills/run.md) (Agent Protocol v0.6.1 — package **4.6.x**).
 
 ```bash
 wikifier session-bootstrap      # one-shot: root, health, attention, actions[]
@@ -85,7 +80,7 @@ Advanced intel as needed: `get_dependencies`, `get_dependents`, `get_cycles`, ba
 
 ## What you get
 
-- **Import analysis** — Python, JS/TS (ESM/CJS, barrels), Rust (`use`/`mod` + best-effort `crate::` paths), Go, C/C++ includes, C# usings; per-edge confidence; barrel expansion for TS/JS
+- **Import analysis** — deep/ACS for Python + JS/TS (ESM/CJS, barrels, CDIA); regex-hint maps for Rust/Go/C/C++/C#/Java; per-edge confidence on the deep path
 - **Incremental pipeline** — pure-Python `update-maps`: dirty parse → import cache → reverse deps → cycles → `library.md`
 - **Warm agent maps (4.6.3–4.6.7)** — zero-dirty + **index-first** candidates (re-list only when fingerprint / map-scoped index / live count disagree); **MapScope** keeps collect, live count, index filter, and prune aligned; **stdlib SQLite**; content-hash dirty
 - **Two path lists** — `map_paths.txt` = map package roots; `monitored_paths.txt` = wiki/health watch (**independent** — wiki file lists never collapse the map)
diff --git a/file_health.json b/file_health.json
index aa847f4..9f5ed49 100644
--- a/file_health.json
+++ b/file_health.json
@@ -1,16 +1,16 @@
 {
   "version": 2,
-  "last_updated": "2026-09-04 06:17:32",
+  "last_updated": "2026-09-11 06:38:37",
   "entries": {
     "skills/run.md": {
       "status": "🟢 Green",
-      "last_updated": "2026-08-27 11:15:12",
-      "reason": "4.6.13 plan WP0–WP7 wiki/protocol aligned",
-      "wiki_content_hash": "sha256:30f6da4a7b46920c1255c339c4c976c43c3323c6a66f03aed9a5e34cca197e04",
-      "source_content_hash": "sha256:30f6da4a7b46920c1255c339c4c976c43c3323c6a66f03aed9a5e34cca197e04",
-      "last_meaningful_edit": "2026-08-27 11:14:42",
-      "last_wiki_refresh": "2026-08-27 11:15:12",
-      "freshness_provenance": "record-meaningful-edit:2026-08-27 11:14:42 | 4.6.13: close-the-loop mark-green; relative monitors; mark-green:2026-08-27 11:15:12 (wiki hash captured); wiki=run.md"
+      "last_updated": "2026-09-11 06:37:25",
+      "reason": "Protocol v0.6.1 notes and language depth table.",
+      "wiki_content_hash": "sha256:4660244d3ed7b22c8d8bdb3e9473a0cafb0e3bff71b1fde7ef392e49cccc2abc",
+      "source_content_hash": "sha256:4660244d3ed7b22c8d8bdb3e9473a0cafb0e3bff71b1fde7ef392e49cccc2abc",
+      "last_meaningful_edit": "2026-09-11 06:37:17",
+      "last_wiki_refresh": "2026-09-11 06:37:25",
+      "freshness_provenance": "record-meaningful-edit:2026-09-11 06:37:17 | Protocol v0.6.1 additive 4.6.x field notes including sqlite-empty vs cache_backend none; language depth table (subid=hon; mark-green:2026-09-11 06:37:25 (wiki hash captured); wiki=run.md"
     },
     "Findings/Milestones-Overview.md": {
       "status": "🟢 Green",
@@ -57,13 +57,13 @@
     },
     "README.md": {
       "status": "🟢 Green",
-      "last_updated": "2026-08-27 11:15:12",
-      "reason": "4.6.13 plan WP0–WP7 wiki/protocol aligned",
-      "wiki_content_hash": "sha256:ea07d5a76184443393d655eb09084e42d7f6d521f0168fe8e56f043b441327e9",
-      "source_content_hash": "sha256:ea07d5a76184443393d655eb09084e42d7f6d521f0168fe8e56f043b441327e9",
-      "last_meaningful_edit": "2026-08-27 11:14:42",
-      "last_wiki_refresh": "2026-08-27 11:15:12",
-      "freshness_provenance": "record-meaningful-edit:2026-08-27 11:14:42 | 4.6.13 test count; mark-green:2026-08-27 11:15:12 (wiki hash captured); wiki=README.md"
+      "last_updated": "2026-09-11 06:37:25",
+      "reason": "Deep/ACS vs regex-hint language table.",
+      "wiki_content_hash": "sha256:10dc0533d5f4db138e593d63173d2d016173976274bf0e47e3ef2d38664d08ff",
+      "source_content_hash": "sha256:10dc0533d5f4db138e593d63173d2d016173976274bf0e47e3ef2d38664d08ff",
+      "last_meaningful_edit": "2026-09-11 06:37:17",
+      "last_wiki_refresh": "2026-09-11 06:37:25",
+      "freshness_provenance": "record-meaningful-edit:2026-09-11 06:37:17 | Language table: deep/ACS vs regex hint; protocol v0.6.1 (subid=honest-map).; mark-green:2026-09-11 06:37:25 (wiki hash captured); wiki=README.md"
     },
     "wikifier/mcp/server.py": {
       "status": "🟢 Green",
@@ -134,23 +134,23 @@
     },
     "CHANGELOG.md": {
       "status": "🟢 Green",
-      "last_updated": "2026-08-27 11:15:12",
-      "reason": "4.6.13 plan WP0–WP7 wiki/protocol aligned",
-      "wiki_content_hash": "sha256:7a0a54cb4ea5a95815dad3dad5d2e841c74b5b1a47e5cc9b193c96e1a50b7b1c",
-      "source_content_hash": "sha256:7a0a54cb4ea5a95815dad3dad5d2e841c74b5b1a47e5cc9b193c96e1a50b7b1c",
-      "last_meaningful_edit": "2026-08-27 11:14:42",
-      "last_wiki_refresh": "2026-08-27 11:15:12",
-      "freshness_provenance": "record-meaningful-edit:2026-08-27 11:14:42 | 4.6.13 Keep a Changelog; mark-green:2026-08-27 11:15:12 (wiki hash captured); wiki=CHANGELOG.md"
+      "last_updated": "2026-09-11 06:37:25",
+      "reason": "Unreleased honesty notes.",
+      "wiki_content_hash": "sha256:3a12d8851eaa663ea26b6997143b39b66efb6768dea5965bbae73e104771dbad",
+      "source_content_hash": "sha256:3a12d8851eaa663ea26b6997143b39b66efb6768dea5965bbae73e104771dbad",
+      "last_meaningful_edit": "2026-09-11 06:37:17",
+      "last_wiki_refresh": "2026-09-11 06:37:25",
+      "freshness_provenance": "record-meaningful-edit:2026-09-11 06:37:17 | Unreleased: library.md honesty, protocol v0.6.1, language table (subid=honest-map).; mark-green:2026-09-11 06:37:25 (wiki hash captured); wiki=CHANGELOG.md"
     },
     "CLAUDE.md": {
       "status": "🟢 Green",
-      "last_updated": "2026-09-04 06:17:32",
-      "reason": "live hash synced; case-ghost Claude.md pruned",
-      "wiki_content_hash": "sha256:aa4eed92d69d7575c1d26beb9cc7852d2596cb771d65cea576374fd425856445",
-      "source_content_hash": "sha256:aa4eed92d69d7575c1d26beb9cc7852d2596cb771d65cea576374fd425856445",
-      "last_meaningful_edit": "2026-09-04 06:17:31",
-      "last_wiki_refresh": "2026-09-04 06:17:32",
-      "freshness_provenance": "record-meaningful-edit:2026-09-04 06:17:31 | re-baseline live hash after Claude.md case-ghost retirement; mark-green:2026-09-04 06:17:32 (wiki hash captured); wiki=CLAUDE.md"
+      "last_updated": "2026-09-11 06:37:25",
+      "reason": "Protocol pointer v0.6.1.",
+      "wiki_content_hash": "sha256:d2a708614ef48b5d1dd0f7bda001f9fff0b65f30f004513200636c00125bcc0d",
+      "source_content_hash": "sha256:d2a708614ef48b5d1dd0f7bda001f9fff0b65f30f004513200636c00125bcc0d",
+      "last_meaningful_edit": "2026-09-11 06:37:17",
+      "last_wiki_refresh": "2026-09-11 06:37:25",
+      "freshness_provenance": "record-meaningful-edit:2026-09-11 06:37:17 | Point agent contract at protocol v0.6.1 (subid=honest-map).; mark-green:2026-09-11 06:37:25 (wiki hash captured); wiki=CLAUDE.md"
     },
     "wikifier/__init__.py": {
       "status": "🟢 Green",
@@ -223,11 +223,13 @@
     },
     "wikifier/library.py": {
       "status": "🟢 Green",
-      "last_updated": "2026-08-01 11:25:15",
-      "reason": "gap amendment 4.6.9 closed-when verified (subid=gap-amendment-closure)",
-      "source_content_hash": "sha256:6312ddc20cd7cd1adef0ec2e5e9818c5030d57ddf1dc49e0384952cf03681ad4",
-      "last_wiki_refresh": "2026-08-01 11:25:15",
-      "freshness_provenance": "upsert:🟡 Yellow (non-freshness path); mark-green:2026-08-01 11:25:15 (wiki hash captured)"
+      "last_updated": "2026-09-11 06:38:32",
+      "reason": "Wiki captions handle **Role:** as well as ## Purpose.",
+      "wiki_content_hash": "sha256:89e1fc5b8dbfddb8306f55135392fb5bf5faa5d2e18177285d89f26a649665b8",
+      "source_content_hash": "sha256:edd02e80508eb135e50681b05307fd2a0e8d269278171f9b2c1d4cf10975a8f6",
+      "last_meaningful_edit": "2026-09-11 06:38:12",
+      "last_wiki_refresh": "2026-09-11 06:38:32",
+      "freshness_provenance": "record-meaningful-edit:2026-09-11 06:38:12 | Match **Role:** wiki captions (colon inside bold) so tree lines are not Role:** leftover (subid=honest-map).; mark-green:2026-09-11 06:38:32 (wiki hash captured); wiki=library.py.wiki.md"
     },
     "wikifier/parsers/javascript.py": {
       "status": "🟢 Green",
@@ -291,9 +293,13 @@
     },
     "library.md": {
       "status": "🟢 Green",
-      "last_updated": "2026-06-10 20:20:38 AEST",
-      "reason": "Verified: endpoint whitelist + Origin/Host 403s + clean shutdown via curl; headless DOM on all 9 projects x 3 modes (exec/static/file): map renders, exec chip + Stop button, no Tailwind, no active errors; 30/30 tests",
-      "source_content_hash": "sha256:f3f717512ac8c856b79d46d5d47906fdb3f2311025be1bc65186bc3b751bbe2e"
+      "last_updated": "2026-09-11 06:38:37",
+      "reason": "Committed map matches live tree after update-maps --full.",
+      "wiki_content_hash": "sha256:5ced31b3d5598e13d38877627603fcd813d425531c1b3b555c80e1a5211afc03",
+      "source_content_hash": "sha256:5ced31b3d5598e13d38877627603fcd813d425531c1b3b555c80e1a5211afc03",
+      "last_meaningful_edit": "2026-09-11 06:38:37",
+      "last_wiki_refresh": "2026-09-11 06:38:37",
+      "freshness_provenance": "record-meaningful-edit:2026-09-11 06:38:37 | Regenerated from full update-maps on live tree; 4.6.10 leftovers gone (subid=honest-map).; mark-green:2026-09-11 06:38:37 (wiki hash captured); wiki=library.md"
     },
     "screenshot/front_page_review.png": {
       "status": "🟢 Green",
@@ -565,12 +571,12 @@
     },
     "wikifier/agent_loop.py": {
       "status": "🟢 Green",
-      "last_updated": "2026-08-27 11:15:11",
-      "reason": "4.6.13 plan WP0–WP7 wiki/protocol aligned",
-      "source_content_hash": "sha256:e08d0f9d3d7ffd57a544277a7ddb7342abd0d216cd4b846f6878b4f1126e7a4a",
-      "last_meaningful_edit": "2026-08-27 11:14:41",
-      "last_wiki_refresh": "2026-08-27 11:15:11",
-      "freshness_provenance": "record-meaningful-edit:2026-08-27 11:14:41 | 4.6.13: emit mark_green action for recorded yellows; mark-green:2026-08-27 11:15:11 (wiki hash captured)"
+      "last_updated": "2026-09-11 06:37:25",
+      "reason": "Bootstrap cache_backend refresh; cache_empty / cache_files_indexed additive.",
+      "source_content_hash": "sha256:feb6a159759552f27af71035557515ca6f367df7e0277df99b769814c27b7893",
+      "last_meaningful_edit": "2026-09-11 06:37:17",
+      "last_wiki_refresh": "2026-09-11 06:37:25",
+      "freshness_provenance": "record-meaningful-edit:2026-09-11 06:37:17 | Refresh cache_backend after ACS persist; add cache_empty and cache_files_indexed so sqlite-empty is not none (subid=hone; mark-green:2026-09-11 06:37:25 (wiki hash captured)"
     },
     "tests/test_agent_loop.py": {
       "status": "🟢 Green",
@@ -971,6 +977,25 @@
       "last_meaningful_edit": "2026-08-27 11:27:44",
       "last_wiki_refresh": "2026-08-27 11:27:44",
       "freshness_provenance": "record-meaningful-edit:2026-08-27 11:27:44 | 4.6.13: status tools wrap health/cache in call_with_deadline; mark-green:2026-08-27 11:27:44 (wiki hash captured); wiki=status_ops.py.wiki.md"
+    },
+    "tests/test_library_map_honesty.py": {
+      "status": "🟢 Green",
+      "last_updated": "2026-09-11 06:38:32",
+      "reason": "Caption **Role:** unit test.",
+      "source_content_hash": "sha256:c9e8e37d44908971ee3167281d1934186d71f8ed97d73ab9019cb1afec616165",
+      "last_meaningful_edit": "2026-09-11 06:38:32",
+      "last_wiki_refresh": "2026-09-11 06:38:32",
+      "freshness_provenance": "record-meaningful-edit:2026-09-11 06:38:32 | Cover **Role:** wiki caption parsing (subid=honest-map).; mark-green:2026-09-11 06:38:32 (wiki hash captured)"
+    },
+    "wikifier/library.py.wiki.md": {
+      "status": "🟢 Green",
+      "last_updated": "2026-09-11 06:37:25",
+      "reason": "Generator wiki current.",
+      "wiki_content_hash": "sha256:89e1fc5b8dbfddb8306f55135392fb5bf5faa5d2e18177285d89f26a649665b8",
+      "source_content_hash": "sha256:89e1fc5b8dbfddb8306f55135392fb5bf5faa5d2e18177285d89f26a649665b8",
+      "last_meaningful_edit": "2026-09-11 06:37:18",
+      "last_wiki_refresh": "2026-09-11 06:37:25",
+      "freshness_provenance": "record-meaningful-edit:2026-09-11 06:37:18 | Wiki for library.md generator: live-path filter and wiki captions (subid=honest-map).; mark-green:2026-09-11 06:37:25 (wiki hash captured); wiki=library.py.wiki.md"
     }
   }
 }
\ No newline at end of file
diff --git a/file_health.md b/file_health.md
index 8ca2187..2fd1131 100644
--- a/file_health.md
+++ b/file_health.md
@@ -5,8 +5,8 @@
 | .github/ISSUE_TEMPLATE/config.yml | 🟢 Green | 2026-08-27 11:15:12 | 4.6.13 plan WP0–WP7 wiki/protocol aligned |
 | .github/workflows/ci.yml | 🟢 Green | 2026-08-27 11:15:12 | 4.6.13 plan WP0–WP7 wiki/protocol aligned |
 | .github/workflows/publish.yml | 🟢 Green | 2026-08-27 11:15:12 | 4.6.13 plan WP0–WP7 wiki/protocol aligned |
-| CHANGELOG.md | 🟢 Green | 2026-08-27 11:15:12 | 4.6.13 plan WP0–WP7 wiki/protocol aligned |
-| CLAUDE.md | 🟢 Green | 2026-09-04 06:17:32 | live hash synced; case-ghost Claude.md pruned |
+| CHANGELOG.md | 🟢 Green | 2026-09-11 06:37:25 | Unreleased honesty notes. |
+| CLAUDE.md | 🟢 Green | 2026-09-11 06:37:25 | Protocol pointer v0.6.1. |
 | CONTRIBUTING.md | 🟢 Green | 2026-08-27 11:15:12 | 4.6.13 plan WP0–WP7 wiki/protocol aligned |
 | Findings/2026-06-10-Dogfood-Refactor-Validation.md | 🟢 Green | 2026-06-10 09:54:26 AEST | Self-describing findings doc |
 | Findings/2026-06-10-Fix-Plan.md | 🟢 Green | 2026-06-10 14:20:33 AEST | Results appended, all phases verified |
@@ -39,16 +39,16 @@
 | Findings/residual-1-5-closure-2026-07-09.md | 🟢 Green | 2026-07-09 08:07:43 | residual-1-5-closure verified; tests OK (subid=residual-1-5-closure) |
 | Logged_issues/2026-06-10-brc-scoped-rerun-pathology.md | 🟢 Green | 2026-06-10 19:09:35 AEST | Verified: 30/30 unittest, exports 8/8, churn 4/4; sh update-maps 3m39s->2.0s + hung incremental now 1.5s; Babylon scoped re-run 75min->80.6s, cache 274MB->101MB; all 12 sh commands smoke-tested |
 | Logged_issues/2026-06-10-js-barrel-churn-selftest-failure.md | 🟢 Green | 2026-06-10 14:19:50 AEST | v4.2.0 fix pass verified: 28/28 unittest, parser self-tests (churn 4/4), llama_index 3837/3837 files 8.5s, Babylon 3905/3905, RecipeLab library.md recovered, redox honest reporting, health CLI flags, MCP smoke. |
-| README.md | 🟢 Green | 2026-08-27 11:15:12 | 4.6.13 plan WP0–WP7 wiki/protocol aligned |
+| README.md | 🟢 Green | 2026-09-11 06:37:25 | Deep/ACS vs regex-hint language table. |
 | diagnostics.html | 🟢 Green | 2026-06-05 08:33:20 AEST | Wiki summary verified accurate after change. |
 | file_health.md | 🟢 Green | 2026-06-07 12:47:31 AEST | Phase 1 cruft pruning complete (bulk historical M2-M4/Logged/etc removed per audit). Survivors re-marked Green. subid=simplification-cruft-phase-1. |
 | index.html | 🟢 Green | 2026-06-11 00:20:17 AEST | Verified: 30/30 tests; tree generated on all 9 projects (llvm 2,940 files renders as clean indented tree); headless 9/9 tree-ok + lazy graph + forced-open render + pan-zoom canvas + file:// banner; parser comment-leak repro now 0 garbage edges |
-| library.md | 🟢 Green | 2026-06-10 20:20:38 AEST | Verified: endpoint whitelist + Origin/Host 403s + clean shutdown via curl; headless DOM on all 9 projects x 3 modes (exec/static/file): map renders, exec chip + Stop button, no Tailwind, no active errors; 30/30 tests |
+| library.md | 🟢 Green | 2026-09-11 06:38:37 | Committed map matches live tree after update-maps --full. |
 | map_paths.txt | 🟢 Green | 2026-07-12 13:26:29 | 4.6.6 verified |
 | monitored_paths.txt | 🟢 Green | 2026-08-27 11:15:12 | 4.6.13 plan WP0–WP7 wiki/protocol aligned |
 | pyproject.toml | 🟢 Green | 2026-06-10 14:41:19 AEST | Build + twine check pass; clean-room wheel install verified |
 | screenshot/front_page_review.png | 🟢 Green | 2026-06-11 00:37:47 AEST | Asset referenced by README |
-| skills/run.md | 🟢 Green | 2026-08-27 11:15:12 | 4.6.13 plan WP0–WP7 wiki/protocol aligned |
+| skills/run.md | 🟢 Green | 2026-09-11 06:37:25 | Protocol v0.6.1 notes and language depth table. |
 | tests/ | 🟢 Green | 2026-06-10 16:59:05 AEST | Verified: 30/30 unittest, exports 8/8, churn 4/4; Babylon full run 25m52s->5m52s and 417k->44k edges; worst file 990->55; RecipeLab identical 671 edges; e2e cache carries imported_names + barrel_leaf_selection |
 | tests/__init__.py | 🟢 Green | 2026-07-09 06:34:55 | hygiene session complete 4.5.6; 53 tests OK |
 | tests/_base.py | 🟢 Green | 2026-07-09 06:34:55 | hygiene session complete 4.5.6; 53 tests OK |
@@ -69,6 +69,7 @@
 | tests/test_health.py | 🟢 Green | 2026-08-27 11:15:12 | 4.6.13 plan WP0–WP7 wiki/protocol aligned |
 | tests/test_import_cache.py | 🟢 Green | 2026-08-13 17:08:27 | Persist-path reverse increment test green. |
 | tests/test_index_map_paths.py | 🟢 Green | 2026-07-12 13:41:02 | 125 unittest OK |
+| tests/test_library_map_honesty.py | 🟢 Green | 2026-09-11 06:38:32 | Caption **Role:** unit test. |
 | tests/test_multi_lang_parsers.py | 🟢 Green | 2026-07-09 06:34:55 | hygiene session complete 4.5.6; 53 tests OK |
 | tests/test_parsers.py | 🟢 Green | 2026-07-09 06:34:55 | hygiene session complete 4.5.6; 53 tests OK |
 | tests/test_plan_2026_08_27.py | 🟢 Green | 2026-08-27 11:27:44 | deadline tests wiki |
@@ -79,7 +80,7 @@
 | wikifier.sh | 🟢 Green | 2026-08-01 11:25:19 | gap amendment 4.6.9 closed-when verified (subid=gap-amendment-closure) |
 | wikifier/__init__.py | 🟢 Green | 2026-08-27 11:15:12 | 4.6.13 plan WP0–WP7 wiki/protocol aligned |
 | wikifier/__main__.py | 🟢 Green | 2026-07-09 06:34:55 | hygiene session complete 4.5.6; 53 tests OK |
-| wikifier/agent_loop.py | 🟢 Green | 2026-08-27 11:15:11 | 4.6.13 plan WP0–WP7 wiki/protocol aligned |
+| wikifier/agent_loop.py | 🟢 Green | 2026-09-11 06:37:25 | Bootstrap cache_backend refresh; cache_empty / cache_files_indexed additive. |
 | wikifier/api.py | 🟢 Green | 2026-08-27 11:15:11 | 4.6.13 plan WP0–WP7 wiki/protocol aligned |
 | wikifier/cache/__init__.py | 🟢 Green | 2026-08-13 16:51:15 | Named cache package exports real io/files/graph/cycles/acs/barrel. |
 | wikifier/cache/_core.py | 🟢 Green | 2026-08-27 11:15:12 | 4.6.13 plan WP0–WP7 wiki/protocol aligned |
@@ -95,7 +96,8 @@
 | wikifier/health_pkg/__init__.py | 🟢 Green | 2026-08-27 11:15:12 | 4.6.13 plan WP0–WP7 wiki/protocol aligned |
 | wikifier/import_cache.py | 🟢 Green | 2026-09-04 06:16:42 | wiki + baseline after shim confirmation; tests OK |
 | wikifier/index.html | 🟢 Green | 2026-06-11 00:20:18 AEST | Verified: 30/30 tests; tree generated on all 9 projects (llvm 2,940 files renders as clean indented tree); headless 9/9 tree-ok + lazy graph + forced-open render + pan-zoom canvas + file:// banner; parser comment-leak repro now 0 garbage edges |
-| wikifier/library.py | 🟢 Green | 2026-08-01 11:25:15 | gap amendment 4.6.9 closed-when verified (subid=gap-amendment-closure) |
+| wikifier/library.py | 🟢 Green | 2026-09-11 06:38:32 | Wiki captions handle **Role:** as well as ## Purpose. |
+| wikifier/library.py.wiki.md | 🟢 Green | 2026-09-11 06:37:25 | Generator wiki current. |
 | wikifier/locking.py | 🟢 Green | 2026-08-01 11:25:14 | gap amendment 4.6.9 closed-when verified (subid=gap-amendment-closure) |
 | wikifier/mcp/README.md | 🟢 Green | 2026-07-09 08:51:23 | 4.6.2 polish+dogfood verified 74 tests (subid=agent-ideal-loop-polish) |
 | wikifier/mcp/__init__.py | 🟢 Green | 2026-06-10 09:27:38 AEST | Refactor verified: py_compile + no-mcp/no-fcntl import sims + parser self-tests + check-changes/update-maps/health smoke all pass. Interface unchanged. |
diff --git a/journal/2026/09/11.md b/journal/2026/09/11.md
new file mode 100644
index 0000000..c4a092c
--- /dev/null
+++ b/journal/2026/09/11.md
@@ -0,0 +1,44 @@
+## [2026-09-11 06:37:17] record-change
+**File:** wikifier/library.py
+**Reason:** Omit missing-on-disk cache keys from library.md; wiki captions not health audit reasons (subid=honest-map).
+
+## [2026-09-11 06:37:17] record-change
+**File:** wikifier/agent_loop.py
+**Reason:** Refresh cache_backend after ACS persist; add cache_empty and cache_files_indexed so sqlite-empty is not none (subid=honest-map).
+
+## [2026-09-11 06:37:17] record-change
+**File:** tests/test_library_map_honesty.py
+**Reason:** Test library.md names only live files; generator drops ghosts; bootstrap sqlite-empty vs none (subid=honest-map).
+
+## [2026-09-11 06:37:17] record-change
+**File:** skills/run.md
+**Reason:** Protocol v0.6.1 additive 4.6.x field notes including sqlite-empty vs cache_backend none; language depth table (subid=honest-map).
+
+## [2026-09-11 06:37:17] record-change
+**File:** README.md
+**Reason:** Language table: deep/ACS vs regex hint; protocol v0.6.1 (subid=honest-map).
+
+## [2026-09-11 06:37:17] record-change
+**File:** CHANGELOG.md
+**Reason:** Unreleased: library.md honesty, protocol v0.6.1, language table (subid=honest-map).
+
+## [2026-09-11 06:37:17] record-change
+**File:** CLAUDE.md
+**Reason:** Point agent contract at protocol v0.6.1 (subid=honest-map).
+
+## [2026-09-11 06:37:18] record-change
+**File:** wikifier/library.py.wiki.md
+**Reason:** Wiki for library.md generator: live-path filter and wiki captions (subid=honest-map).
+
+## [2026-09-11 06:38:12] record-change
+**File:** wikifier/library.py
+**Reason:** Match **Role:** wiki captions (colon inside bold) so tree lines are not Role:** leftover (subid=honest-map).
+
+## [2026-09-11 06:38:32] record-change
+**File:** tests/test_library_map_honesty.py
+**Reason:** Cover **Role:** wiki caption parsing (subid=honest-map).
+
+## [2026-09-11 06:38:37] record-change
+**File:** library.md
+**Reason:** Regenerated from full update-maps on live tree; 4.6.10 leftovers gone (subid=honest-map).
+
diff --git a/library.md b/library.md
index 1cb5d4c..b85099f 100644
--- a/library.md
+++ b/library.md
@@ -5,173 +5,164 @@
 
 ## File Tree
 
-> Every parsed/tracked file, organised by folder. Descriptions come from
-> the agent wiki (file_health). The dependency graph is further below.
+> Every parsed/tracked file, organised by folder. Captions come from
+> `*.wiki.md` purpose/role text when present. Health *reasons* are audit
+> stamps and are not copied here. The dependency graph is further below.
 
 ```text
-Wikifier/  (133 files)
+workspace/  (129 files)
 ├── .github/
+│   ├── ISSUE_TEMPLATE/
+│   │   └── config.yml
 │   └── workflows/
-│       └── publish.yml — Verified: bash -n, dynamic banner shows v4.2.0 from package, YAML parses, 28/28 tests, pac…
+│       ├── ci.yml
+│       └── publish.yml
 ├── Findings/
-│   ├── 2026-06-10-Dogfood-Refactor-Validation.md — Self-describing findings doc
-│   ├── 2026-06-10-Fix-Plan.md — Results appended, all phases verified
-│   ├── 2026-08-13-implementation-plan.md — implementation plan
-│   ├── 2026-08-13-research-01-parsers.md — Research findings saved.
-│   ├── 2026-08-13-research-02-cache-graph.md — Research findings saved.
-│   ├── 2026-08-13-research-03-health-protocol.md — Research findings saved.
-│   ├── 2026-08-13-research-04-mcp-cli.md — Research findings saved.
-│   ├── 2026-08-13-research-05-packaging-tests.md — Research findings saved.
-│   ├── 2026-08-27-plan.md — 2026-08-27-plan: proposed 4.6.13 follow-up from five-slice research; not executed
-│   ├── M5-Dogfood-Assessment-Report.md — kept; stale yellow cleared
-│   ├── M5-Dogfood-Progress.md — kept; stale yellow cleared
-│   ├── M5.1-cross-hardening-analysis.md — kept; stale yellow cleared
-│   ├── Milestones-Overview.md — kept; stale yellow cleared
-│   ├── agent-first-ideal-loop-2026-07-09.md — 4.6.1 content-honest legacy fix verified (subid=agent-ideal-loop)
-│   ├── agent-ideal-loop-polish-dogfood-2026-07-09.md — 4.6.2 polish+dogfood verified 74 tests (subid=agent-ideal-loop-polish)
-│   ├── agent-scale-perf-accuracy-2026-07-12.md — findings recorded
-│   ├── agent-scale-sqlite-coverage-2026-07-12.md — 4.6.4 sqlite coverage verified 93 tests
-│   ├── agent-walk-coverage-cache-2026-07-12.md — findings updated
-│   ├── dogfood-goal-pass1-2026-07-09.json — goal verification complete
-│   ├── dogfood-goal-pass2-2026-07-09.json — goal verification complete
-│   ├── dogfood-hygiene-fix-2026-07-09.json — verified 53 tests; dogfood validate 0/8
-│   ├── dogfood-hygiene-fix-2026-07-09.md — verified 53 tests; dogfood validate 0/8
-│   ├── gap-amendment-closure-2026-08-01.md — gap amendment 4.6.9 closed-when verified (subid=gap-amendment-closure)
-│   ├── gap-amendment-plan-2026-08-01.md — gap amendment 4.6.9 closed-when verified (subid=gap-amendment-closure)
-│   ├── gap-closure-report.md — G12 closed; 39/39 tests
-│   ├── index-first-map-paths-2026-07-12.md — evidence updated
-│   ├── long-horizon-autonomous-ops.md — goal verification complete
-│   ├── p6_real_world_validation_report.md — kept; stale yellow cleared
-│   └── residual-1-5-closure-2026-07-09.md — residual-1-5-closure verified; tests OK (subid=residual-1-5-closure)
+│   ├── 2026-06-10-Dogfood-Refactor-Validation.md
+│   ├── 2026-06-10-Fix-Plan.md
+│   ├── 2026-08-13-implementation-plan.md
+│   ├── 2026-08-13-research-01-parsers.md
+│   ├── 2026-08-13-research-02-cache-graph.md
+│   ├── 2026-08-13-research-03-health-protocol.md
+│   ├── 2026-08-13-research-04-mcp-cli.md
+│   ├── 2026-08-13-research-05-packaging-tests.md
+│   ├── 2026-08-27-plan.md
+│   ├── M5-Dogfood-Assessment-Report.md
+│   ├── M5-Dogfood-Progress.md
+│   ├── M5.1-cross-hardening-analysis.md
+│   ├── Milestones-Overview.md
+│   ├── agent-first-ideal-loop-2026-07-09.md
+│   ├── agent-ideal-loop-polish-dogfood-2026-07-09.md
+│   ├── agent-scale-perf-accuracy-2026-07-12.md
+│   ├── agent-scale-sqlite-coverage-2026-07-12.md
+│   ├── agent-walk-coverage-cache-2026-07-12.md
+│   ├── dogfood-goal-pass1-2026-07-09.json
+│   ├── dogfood-goal-pass2-2026-07-09.json
+│   ├── dogfood-hygiene-fix-2026-07-09.json
+│   ├── dogfood-hygiene-fix-2026-07-09.md
+│   ├── gap-amendment-closure-2026-08-01.md
+│   ├── gap-amendment-plan-2026-08-01.md
+│   ├── gap-closure-report.md
+│   ├── index-first-map-paths-2026-07-12.md
+│   ├── long-horizon-autonomous-ops.md
+│   ├── p6_real_world_validation_report.md
+│   └── residual-1-5-closure-2026-07-09.md
 ├── Logged_issues/
-│   ├── 2026-06-10-brc-scoped-rerun-pathology.md — Verified: 30/30 unittest, exports 8/8, churn 4/4; sh update-maps 3m39s->2.0s + hung increm…
-│   └── 2026-06-10-js-barrel-churn-selftest-failure.md — v4.2.0 fix pass verified: 28/28 unittest, parser self-tests (churn 4/4), llama_index 3837/…
+│   ├── 2026-06-10-brc-scoped-rerun-pathology.md
+│   └── 2026-06-10-js-barrel-churn-selftest-failure.md
 ├── screenshot/
-│   └── front_page_review.png — Asset referenced by README
+│   └── front_page_review.png
 ├── skills/
-│   └── run.md — gap amendment 4.6.9 closed-when verified (subid=gap-amendment-closure)
+│   └── run.md
 ├── tests/
 │   ├── selftest/
-│   │   ├── __init__.py — hygiene session complete 4.5.6; 53 tests OK
-│   │   ├── run_cdia_selftest.py — hygiene session complete 4.5.6; 53 tests OK
-│   │   ├── run_contracts_selftest.py — hygiene session complete 4.5.6; 53 tests OK
-│   │   ├── run_javascript_selftest.py — hygiene session complete 4.5.6; 53 tests OK
-│   │   ├── run_python_parser_selftest.py — hygiene session complete 4.5.6; 53 tests OK
-│   │   └── run_resolution_selftest.py — hygiene session complete 4.5.6; 53 tests OK
-│   ├── __init__.py — hygiene session complete 4.5.6; 53 tests OK
-│   ├── _base.py — hygiene session complete 4.5.6; 53 tests OK
-│   ├── run_all.py — hygiene session complete 4.5.6; 53 tests OK
-│   ├── test_agent_loop.py — 4.6.2 polish+dogfood verified 74 tests (subid=agent-ideal-loop-polish)
-│   ├── test_agent_scale.py — ACS persist regression green
-│   ├── test_agent_surface_contracts.py — PEP585 future-import scan covers javascript.py.
-│   ├── test_barrel_invalidation.py — unskipped content-honest barrel tests
-│   ├── test_cache_store.py — instrumented warm load assertion
-│   ├── test_gap_amendment_2026_08.py — gap amendment 4.6.9 closed-when verified (subid=gap-amendment-closure)
-│   ├── test_gap_closure.py — content changed since last trusted baseline (check_changes content-honest)
-│   ├── test_health.py — hygiene session complete 4.5.6; 53 tests OK
-│   ├── test_import_cache.py — Persist-path reverse increment test green.
-│   ├── test_index_map_paths.py — 125 unittest OK
+│   │   ├── __init__.py
+│   │   ├── run_cdia_selftest.py
+│   │   ├── run_contracts_selftest.py
+│   │   ├── run_javascript_selftest.py
+│   │   ├── run_python_parser_selftest.py
+│   │   └── run_resolution_selftest.py
+│   ├── __init__.py
+│   ├── _base.py
+│   ├── run_all.py
+│   ├── test_agent_loop.py
+│   ├── test_agent_scale.py
+│   ├── test_agent_surface_contracts.py
+│   ├── test_barrel_invalidation.py
+│   ├── test_cache_store.py
+│   ├── test_gap_amendment_2026_08.py
+│   ├── test_gap_closure.py — Gap-closure regressions — G4 ACS actionable low-conf, G5 health module vs `wikifier.health…
+│   ├── test_health.py
+│   ├── test_import_cache.py
+│   ├── test_index_map_paths.py
 │   ├── test_init_seed.py
-│   ├── test_multi_lang_parsers.py — hygiene session complete 4.5.6; 53 tests OK
-│   ├── test_parsers.py — hygiene session complete 4.5.6; 53 tests OK
+│   ├── test_library_map_honesty.py
+│   ├── test_multi_lang_parsers.py
+│   ├── test_parsers.py
 │   ├── test_plan_2026_08_27.py
-│   ├── test_selftest_wrappers.py — G12 closed; 39/39 tests
-│   └── test_walk_coverage_resolvers.py — poison test green
-├── wikifier/  (60 files)
+│   ├── test_selftest_wrappers.py
+│   └── test_walk_coverage_resolvers.py
+├── wikifier/  (53 files)
 │   ├── cache/
-│   │   ├── __init__.py — Named cache package exports real io/files/graph/cycles/acs/barrel.
-│   │   ├── _core.py — content changed since last trusted baseline (check_changes content-honest)
+│   │   ├── __init__.py
+│   │   ├── _core.py
 │   │   ├── acs.py
 │   │   ├── barrel.py
 │   │   ├── cycles.py
 │   │   ├── diagnostics.py
-│   │   ├── files.py — Real file ops + same-second dirty
+│   │   ├── files.py — File entries, `sha256:` content hash, `compute_files_needing_reparse` (light index; same-s…
 │   │   ├── graph.py
-│   │   ├── io.py — Real cache I/O
+│   │   ├── io.py — SQLite-primary `load_cache` / `save_cache` / `load_mtime_index`. Legacy JSON dual-read onl…
 │   │   └── streaming.py
 │   ├── health_pkg/
-│   │   └── __init__.py — content changed since last trusted baseline (check_changes content-honest)
+│   │   └── __init__.py
 │   ├── mcp/
 │   │   ├── tools/
-│   │   │   ├── __init__.py — content changed since last trusted baseline (check_changes content-honest)
-│   │   │   ├── _common.py — Slim helpers; no second FastMCP.
-│   │   │   ├── intel.py — DELETED — path missing on disk (check_changes ghost detection)
-│   │   │   ├── status.py — DELETED — path missing on disk (check_changes ghost detection)
-│   │   │   └── workflow.py — DELETED — path missing on disk (check_changes ghost detection)
-│   │   ├── README.md — 4.6.2 polish+dogfood verified 74 tests (subid=agent-ideal-loop-polish)
-│   │   ├── __init__.py — Refactor verified: py_compile + no-mcp/no-fcntl import sims + parser self-tests + check-ch…
-│   │   ├── deadline.py
-│   │   ├── server.py — wikifier-mcp main restored via server_impl
-│   │   ├── server_backup.py
-│   │   └── server_impl.py — content change or no baseline (check_changes content-honest auto-detect)
+│   │   │   ├── __init__.py
+│   │   │   └── _common.py
+│   │   ├── README.md
+│   │   ├── __init__.py
+│   │   ├── deadline.py — Stdlib in-process wall-clock cap for MCP tools (`call_with_deadline`, `MCP_INPROCESS_DEADL…
+│   │   ├── server.py — Installed MCP entry (`wikifier-mcp`, `python -m wikifier.mcp.server`). Re-exports `mcp` + …
+│   │   ├── server_impl.py
+│   │   └── status_ops.py — Library health/cache work for MCP get_project_status and get_files_needing_attention, wrap…
 │   ├── parsers/
 │   │   ├── bree/
-│   │   │   ├── __init__.py — content change or no baseline (check_changes content-honest auto-detect)
-│   │   │   └── _bree.py
-│   │   ├── javascript/
 │   │   │   ├── __init__.py
-│   │   │   └── _parser.py
-│   │   ├── __init__.py — lazy language imports
-│   │   ├── _edge.py — content changed since last trusted baseline (check_changes content-honest)
-│   │   ├── _ldsi.py
-│   │   ├── bree.py
-│   │   ├── c_cpp.py — content changed since last trusted baseline (check_changes content-honest)
-│   │   ├── cdia.py — mtime-only / post-4.5.x auto-yellow cleared; git content clean at mark-green (hygiene sess…
-│   │   ├── csharp.py — 4.6.5 verified
-│   │   ├── go_lang.py — 4.6.4 sqlite coverage verified 93 tests
-│   │   ├── java.py — hygiene session complete 4.5.6; 53 tests OK
-│   │   ├── javascript.py — content changed since last trusted baseline (check_changes content-honest)
-│   │   ├── python.py — content changed since last trusted baseline (check_changes content-honest)
-│   │   └── rust.py — crate resolve unit tested
+│   │   │   └── _bree.py
+│   │   ├── __init__.py
+│   │   ├── _edge.py
+│   │   ├── _ldsi.py — Shared LDSI helpers (`_extract_balanced_argument`, `_extract_candidate_literals`, `_analyz…
+│   │   ├── c_cpp.py — Zero-dep C/C++ `#include` parser. `parse_c_cpp_imports(filepath)` → edge list for `.c/.h/.…
+│   │   ├── cdia.py
+│   │   ├── csharp.py
+│   │   ├── go_lang.py
+│   │   ├── java.py
+│   │   ├── javascript.py — : JavaScript / TypeScript import parser for Milestone 2 (Dependency Intelligence).
+│   │   ├── python.py — : Core Python import parser for Milestone 2 (Dependency Intelligence).
+│   │   └── rust.py
 │   ├── scripts/
-│   │   ├── wikifier.ps1 — Verified: endpoint whitelist + Origin/Host 403s + clean shutdown via curl; headless DOM on…
-│   │   └── wikifier.sh — synced with root; portable rel paths (subid=post-assess-hygiene)
-│   ├── __init__.py — content changed since last trusted baseline (check_changes content-honest)
-│   ├── __main__.py — hygiene session complete 4.5.6; 53 tests OK
-│   ├── agent_loop.py — content changed since last trusted baseline (check_changes content-honest)
-│   ├── api.py — content changed since last trusted baseline (check_changes content-honest)
-│   ├── cache_store.py — Incremental sqlite upsert
-│   ├── candidates.py — content changed since last trusted baseline (check_changes content-honest)
-│   ├── cli.py — content changed since last trusted baseline (check_changes content-honest)
-│   ├── contracts.py — reserved keys _candidate_list/_map_coverage/_reverse_signature
-│   ├── daemon.py — mtime-only auto-yellow cleared (session tour check-changes); no content edit this session;…
-│   ├── diagnostics.py — hygiene session complete 4.5.6; 53 tests OK
-│   ├── health.py
-│   ├── health_impl.py — content changed since last trusted baseline (check_changes content-honest)
-│   ├── import_cache.py — content changed since last trusted baseline (check_changes content-honest)
-│   ├── import_cache_impl.py
-│   ├── index.html — Verified: 30/30 tests; tree generated on all 9 projects (llvm 2,940 files renders as clean…
-│   ├── library.py — gap amendment 4.6.9 closed-when verified (subid=gap-amendment-closure)
-│   ├── locking.py — gap amendment 4.6.9 closed-when verified (subid=gap-amendment-closure)
-│   ├── project_root.py — residual-1-5-closure verified; tests OK (subid=residual-1-5-closure)
-│   ├── resolution.py — mtime-only / post-4.5.x auto-yellow cleared; git content clean at mark-green (hygiene sess…
-│   └── serve.py — Verified: endpoint whitelist + Origin/Host 403s + clean shutdown via curl; headless DOM on…
-├── CHANGELOG.md — 4.6.10 notes
-├── CLAUDE.md — test count synced to 49
-├── Claude.md — gap amendment 4.6.9 closed-when verified (subid=gap-amendment-closure)
-├── README.md — 4.6.6 verified
-├── diagnostics.html — Wiki summary verified accurate after change.
-├── file_health.md — Phase 1 cruft pruning complete (bulk historical M2-M4/Logged/etc removed per audit). Survi…
-├── index.html — Verified: 30/30 tests; tree generated on all 9 projects (llvm 2,940 files renders as clean…
-├── library.md — Verified: endpoint whitelist + Origin/Host 403s + clean shutdown via curl; headless DOM on…
-├── map_paths.txt — 4.6.6 verified
-├── monitored_paths.txt — 4.6.6 verified
-├── pyproject.toml — Build + twine check pass; clean-room wheel install verified
-├── wikifier.bat — Verified: bash -n, dynamic banner shows v4.2.0 from package, YAML parses, 28/28 tests, pac…
-├── wikifier.ps1 — Verified: endpoint whitelist + Origin/Host 403s + clean shutdown via curl; headless DOM on…
-└── wikifier.sh — gap amendment 4.6.9 closed-when verified (subid=gap-amendment-closure)
+│   │   ├── wikifier.ps1
+│   │   └── wikifier.sh
+│   ├── __init__.py
+│   ├── __main__.py
+│   ├── agent_loop.py
+│   ├── api.py
+│   ├── cache_store.py
+│   ├── candidates.py
+│   ├── cli.py — Hybrid agent CLI. Re-exports `wikifier.api` so `from wikifier.cli import check_changes` wo…
+│   ├── contracts.py
+│   ├── daemon.py
+│   ├── diagnostics.py
+│   ├── health_impl.py
+│   ├── import_cache.py — Backward-compat shim. Real implementation lives in `wikifier.cache` (`from .cache import *…
+│   ├── index.html
+│   ├── library.py — : Pure-Python generator for committed `library.md` (file tree, Mermaid, tables, ACS, rever…
+│   ├── library.py.wiki.md
+│   ├── locking.py
+│   ├── project_root.py
+│   ├── resolution.py
+│   └── serve.py
+├── CHANGELOG.md
+├── CLAUDE.md
+├── CONTRIBUTING.md
+├── README.md
+├── diagnostics.html
+├── file_health.md
+├── index.html
+├── library.md
+├── map_paths.txt
+├── monitored_paths.txt
+├── pyproject.toml
+├── wikifier.bat
+├── wikifier.ps1
+└── wikifier.sh
 ```
 
 ## Dependency Graph (Mermaid)
 
 ```mermaid
 graph TD
-    subgraph root
-        wikifier["wikifier"]
-        wikifier_parsers["wikifier.parsers"]
-        wikifier_parsers_project_root["wikifier.parsers.project_root"]
-        wikifier_parsers_resolution["wikifier.parsers.resolution"]
-    end
     subgraph tests
         tests__base_py["_base.py"]
         tests_run_all_py["run_all.py"]
@@ -191,6 +182,7 @@ graph TD
         tests_test_import_cache_py["test_import_cache.py"]
         tests_test_index_map_paths_py["test_index_map_paths.py"]
         tests_test_init_seed_py["test_init_seed.py"]
+        tests_test_library_map_honesty_py["test_library_map_honesty.py"]
         tests_test_multi_lang_parsers_py["test_multi_lang_parsers.py"]
         tests_test_parsers_py["test_parsers.py"]
         tests_test_plan_2026_08_27_py["test_plan_2026_08_27.py"]
@@ -220,7 +212,6 @@ graph TD
         wikifier_diagnostics_py["diagnostics.py"]
         wikifier_health_impl_py["health_impl.py"]
         wikifier_health_pkg___init___py["__init__.py"]
-        wikifier_health_py["health.py"]
         wikifier_import_cache_py["import_cache.py"]
         wikifier_library_py["library.py"]
         wikifier_locking_py["locking.py"]
@@ -228,10 +219,8 @@ graph TD
         wikifier_mcp_deadline_py["deadline.py"]
         wikifier_mcp_server_impl_py["server_impl.py"]
         wikifier_mcp_server_py["server.py"]
+        wikifier_mcp_status_ops_py["status_ops.py"]
         wikifier_mcp_tools__common_py["_common.py"]
-        wikifier_mcp_tools_intel_py["intel.py"]
-        wikifier_mcp_tools_status_py["status.py"]
-        wikifier_mcp_tools_workflow_py["workflow.py"]
         wikifier_parsers___init___py["__init__.py"]
         wikifier_parsers__edge_py["_edge.py"]
         wikifier_parsers__ldsi_py["_ldsi.py"]
@@ -252,6 +241,8 @@ graph TD
     subgraph External
         _["."]
         __[".."]
+        __project_root["..project_root"]
+        __resolution["..resolution"]
         _wikifier_health_["'wikifier.health'"]
         _wikifier_import_cache_impl_["'wikifier.import_cache_impl'"]
         _wikifier_mcp_server_["'wikifier.mcp.server'"]
@@ -299,6 +290,7 @@ graph TD
         typing["typing"]
         unittest["unittest"]
         warnings["warnings"]
+        wikifier["wikifier"]
         wikifier_agent_loop["wikifier.agent_loop"]
         wikifier_api["wikifier.api"]
         wikifier_cache["wikifier.cache"]
@@ -312,7 +304,8 @@ graph TD
         wikifier_import_cache["wikifier.import_cache"]
         wikifier_library["wikifier.library"]
         wikifier_mcp_deadline["wikifier.mcp.deadline"]
-        wikifier_mcp_server_impl["wikifier.mcp.server_impl"]
+        wikifier_mcp_status_ops["wikifier.mcp.status_ops"]
+        wikifier_parsers["wikifier.parsers"]
         wikifier_parsers_bree["wikifier.parsers.bree"]
         wikifier_parsers_cdia["wikifier.parsers.cdia"]
         wikifier_parsers_javascript["wikifier.parsers.javascript"]
@@ -320,13 +313,6 @@ graph TD
         wikifier_project_root["wikifier.project_root"]
         wikifier_resolution["wikifier.resolution"]
     end
-    wikifier_mcp_server_py --> wikifier_mcp_server_impl_py
-    wikifier_candidates_py -.-> fnmatch
-    wikifier_candidates_py -.-> os
-    wikifier_candidates_py -.-> subprocess
-    wikifier_candidates_py -.-> dataclasses
-    wikifier_candidates_py -.-> pathlib
-    wikifier_candidates_py -.-> typing
     wikifier___init___py -.-> sys
     wikifier___init___py -.-> _
     wikifier___init___py --> wikifier_cli_py
@@ -339,12 +325,79 @@ graph TD
     wikifier_agent_loop_py --> wikifier_project_root_py
     wikifier_agent_loop_py -.-> _
     wikifier_agent_loop_py -. ? .-> _wikifier_health_
+    wikifier_api_py -.-> os
+    wikifier_api_py -.-> sys
+    wikifier_api_py -.-> platform
+    wikifier_api_py -.-> subprocess
+    wikifier_api_py -.-> shutil
+    wikifier_api_py -.-> pathlib
+    wikifier_api_py -.-> typing
+    wikifier_api_py -.-> contextlib
+    wikifier_api_py --> wikifier_project_root_py
+    wikifier_api_py --> wikifier_candidates_py
+    wikifier_api_py --> wikifier_contracts_py
+    wikifier_api_py -.-> datetime
+    wikifier_api_py -.-> _
+    wikifier_api_py --> wikifier_library_py
+    wikifier_api_py --> wikifier_parsers___init___py
+    wikifier_api_py --> wikifier_resolution_py
+    wikifier_api_py --> wikifier_agent_loop_py
+    wikifier_api_py -.-> importlib_resources
+    wikifier_cache___init___py --> wikifier_cache_io_py
+    wikifier_cache___init___py --> wikifier_cache_files_py
+    wikifier_cache___init___py --> wikifier_cache_graph_py
+    wikifier_cache___init___py --> wikifier_cache_cycles_py
+    wikifier_cache___init___py --> wikifier_cache_acs_py
+    wikifier_cache___init___py --> wikifier_cache_barrel_py
+    wikifier_cache___init___py --> wikifier_cache_diagnostics_py
+    wikifier_cache___init___py --> wikifier_cache_streaming_py
+    wikifier_cache___init___py --> wikifier_contracts_py
+    wikifier_cache__core_py -.-> json
+    wikifier_cache__core_py -.-> os
+    wikifier_cache__core_py -.-> time
+    wikifier_cache__core_py -.-> hashlib
+    wikifier_cache__core_py -.-> pathlib
+    wikifier_cache__core_py -.-> typing
+    wikifier_cache__core_py -.-> collections
+    wikifier_cache__core_py -.-> datetime
+    wikifier_cache__core_py -.-> __
+    wikifier_cache__core_py --> wikifier_contracts_py
+    wikifier_cache__core_py --> wikifier_resolution_py
+    wikifier_cache__core_py --> wikifier_cache_io_py
+    wikifier_cache__core_py --> wikifier_cache_files_py
+    wikifier_cache__core_py --> wikifier_parsers_bree___init___py
+    wikifier_cache__core_py -.-> dataclasses
+    wikifier_cache__core_py --> wikifier_project_root_py
+    wikifier_cache__core_py --> wikifier_parsers___init___py
+    wikifier_cache_acs_py --> wikifier_cache__core_py
+    wikifier_cache_barrel_py --> wikifier_cache__core_py
+    wikifier_cache_cycles_py --> wikifier_cache__core_py
+    wikifier_cache_diagnostics_py --> wikifier_cache__core_py
+    wikifier_cache_files_py -.-> hashlib
+    wikifier_cache_files_py -.-> pathlib
+    wikifier_cache_files_py -.-> typing
+    wikifier_cache_files_py --> wikifier_cache_io_py
+    wikifier_cache_graph_py --> wikifier_cache__core_py
+    wikifier_cache_io_py -.-> json
+    wikifier_cache_io_py -.-> os
+    wikifier_cache_io_py -.-> sys
+    wikifier_cache_io_py -.-> traceback
+    wikifier_cache_io_py -.-> pathlib
+    wikifier_cache_io_py -.-> typing
+    wikifier_cache_io_py -.-> __
+    wikifier_cache_streaming_py --> wikifier_cache__core_py
     wikifier_cache_store_py -.-> json
     wikifier_cache_store_py -.-> os
     wikifier_cache_store_py -.-> sqlite3
     wikifier_cache_store_py -.-> contextlib
     wikifier_cache_store_py -.-> pathlib
     wikifier_cache_store_py -.-> typing
+    wikifier_candidates_py -.-> fnmatch
+    wikifier_candidates_py -.-> os
+    wikifier_candidates_py -.-> subprocess
+    wikifier_candidates_py -.-> dataclasses
+    wikifier_candidates_py -.-> pathlib
+    wikifier_candidates_py -.-> typing
     wikifier_cli_py -.-> json
     wikifier_cli_py -.-> os
     wikifier_cli_py -.-> platform
@@ -374,21 +427,22 @@ graph TD
     wikifier_daemon_py -.-> pathlib
     wikifier_daemon_py -.-> typing
     wikifier_daemon_py --> wikifier_cli_py
-    wikifier_daemon_py -.-> wikifier
+    wikifier_daemon_py -.-> _
     wikifier_diagnostics_py -.-> json
     wikifier_diagnostics_py -.-> dataclasses
     wikifier_diagnostics_py -.-> enum
     wikifier_diagnostics_py -.-> typing
-    wikifier_health_py -.-> hashlib
-    wikifier_health_py -.-> json
-    wikifier_health_py -.-> os
-    wikifier_health_py -.-> re
-    wikifier_health_py -.-> sys
-    wikifier_health_py -.-> dataclasses
-    wikifier_health_py -.-> datetime
-    wikifier_health_py -.-> pathlib
-    wikifier_health_py -.-> typing
-    wikifier_health_py -.-> wikifier
+    wikifier_health_impl_py -.-> hashlib
+    wikifier_health_impl_py -.-> json
+    wikifier_health_impl_py -.-> os
+    wikifier_health_impl_py -.-> re
+    wikifier_health_impl_py -.-> sys
+    wikifier_health_impl_py -.-> dataclasses
+    wikifier_health_impl_py -.-> datetime
+    wikifier_health_impl_py -.-> pathlib
+    wikifier_health_impl_py -.-> typing
+    wikifier_health_impl_py -.-> _
+    wikifier_health_pkg___init___py --> wikifier_health_impl_py
     wikifier_import_cache_py --> wikifier_cache___init___py
     wikifier_library_py -.-> json
     wikifier_library_py -.-> os
@@ -406,11 +460,58 @@ graph TD
     wikifier_locking_py -.-> pathlib
     wikifier_locking_py -.-> typing
     wikifier_mcp___init___py --> wikifier_mcp_server_py
+    wikifier_mcp_deadline_py -.-> os
+    wikifier_mcp_deadline_py -.-> threading
+    wikifier_mcp_deadline_py -.-> typing
+    wikifier_mcp_server_py --> wikifier_mcp_server_impl_py
+    wikifier_mcp_server_impl_py -.-> subprocess
+    wikifier_mcp_server_impl_py -.-> re
+    wikifier_mcp_server_impl_py -.-> os
+    wikifier_mcp_server_impl_py -.-> sys
+    wikifier_mcp_server_impl_py -.-> json
+    wikifier_mcp_server_impl_py -.-> wikifier_import_cache
+    wikifier_mcp_server_impl_py -.-> time
+    wikifier_mcp_server_impl_py -.-> importlib
+    wikifier_mcp_server_impl_py -.-> argparse
+    wikifier_mcp_server_impl_py -.-> mcp_server_fastmcp
+    wikifier_mcp_server_impl_py -.-> pydantic
+    wikifier_mcp_server_impl_py -.-> pathlib
+    wikifier_mcp_server_impl_py -.-> typing
+    wikifier_mcp_server_impl_py -.-> datetime
+    wikifier_mcp_server_impl_py --> wikifier_mcp_deadline_py
+    wikifier_mcp_server_impl_py --> wikifier_mcp_status_ops_py
+    wikifier_mcp_server_impl_py -.-> wikifier_cli
+    wikifier_mcp_server_impl_py -. ? .-> _wikifier_health_
+    wikifier_mcp_status_ops_py -.-> importlib
+    wikifier_mcp_status_ops_py -.-> wikifier_import_cache
+    wikifier_mcp_status_ops_py -.-> pathlib
+    wikifier_mcp_status_ops_py -.-> typing
+    wikifier_mcp_status_ops_py --> wikifier_mcp_deadline_py
+    wikifier_mcp_status_ops_py -. ? .-> _wikifier_health_
+    wikifier_mcp_tools__common_py -.-> pathlib
+    wikifier_mcp_tools__common_py -.-> typing
+    wikifier_mcp_tools__common_py -.-> wikifier_api
     wikifier_parsers___init___py -.-> typing
     wikifier_parsers___init___py -.-> importlib
     wikifier_parsers___init___py -. ? .-> modname____name__
     wikifier_parsers__edge_py -.-> typing
     wikifier_parsers__edge_py --> wikifier_contracts_py
+    wikifier_parsers__ldsi_py -.-> re
+    wikifier_parsers__ldsi_py -.-> typing
+    wikifier_parsers_bree___init___py --> wikifier_parsers_bree__bree_py
+    wikifier_parsers_bree__bree_py -.-> json
+    wikifier_parsers_bree__bree_py -.-> re
+    wikifier_parsers_bree__bree_py -.-> warnings
+    wikifier_parsers_bree__bree_py -.-> hashlib
+    wikifier_parsers_bree__bree_py -.-> os
+    wikifier_parsers_bree__bree_py -.-> time
+    wikifier_parsers_bree__bree_py -.-> dataclasses
+    wikifier_parsers_bree__bree_py -.-> pathlib
+    wikifier_parsers_bree__bree_py -.-> typing
+    wikifier_parsers_bree__bree_py -.-> __project_root
+    wikifier_parsers_bree__bree_py -.-> __resolution
+    wikifier_parsers_bree__bree_py -.-> wikifier_resolution
+    wikifier_parsers_bree__bree_py -.-> __
     wikifier_parsers_c_cpp_py -.-> re
     wikifier_parsers_c_cpp_py -.-> pathlib
     wikifier_parsers_c_cpp_py -.-> typing
@@ -489,146 +590,15 @@ graph TD
     wikifier_serve_py -.-> http_server
     wikifier_serve_py -.-> pathlib
     wikifier_serve_py --> wikifier_cli_py
-    wikifier_serve_py -.-> wikifier
-    wikifier_api_py -.-> os
-    wikifier_api_py -.-> sys
-    wikifier_api_py -.-> platform
-    wikifier_api_py -.-> subprocess
-    wikifier_api_py -.-> shutil
-    wikifier_api_py -.-> pathlib
-    wikifier_api_py -.-> typing
-    wikifier_api_py -.-> contextlib
-    wikifier_api_py --> wikifier_project_root_py
-    wikifier_api_py --> wikifier_candidates_py
-    wikifier_api_py --> wikifier_contracts_py
-    wikifier_api_py -.-> datetime
-    wikifier_api_py -.-> _
-    wikifier_api_py --> wikifier_library_py
-    wikifier_api_py --> wikifier_parsers___init___py
-    wikifier_api_py --> wikifier_resolution_py
-    wikifier_api_py --> wikifier_agent_loop_py
-    wikifier_api_py -.-> importlib_resources
-    wikifier_cache___init___py --> wikifier_cache_io_py
-    wikifier_cache___init___py --> wikifier_cache_files_py
-    wikifier_cache___init___py --> wikifier_cache_graph_py
-    wikifier_cache___init___py --> wikifier_cache_cycles_py
-    wikifier_cache___init___py --> wikifier_cache_acs_py
-    wikifier_cache___init___py --> wikifier_cache_barrel_py
-    wikifier_cache___init___py --> wikifier_cache_diagnostics_py
-    wikifier_cache___init___py --> wikifier_cache_streaming_py
-    wikifier_cache___init___py --> wikifier_contracts_py
-    wikifier_cache_files_py -.-> hashlib
-    wikifier_cache_files_py -.-> pathlib
-    wikifier_cache_files_py -.-> typing
-    wikifier_cache_files_py --> wikifier_cache_io_py
-    wikifier_cache_io_py -.-> json
-    wikifier_cache_io_py -.-> os
-    wikifier_cache_io_py -.-> sys
-    wikifier_cache_io_py -.-> traceback
-    wikifier_cache_io_py -.-> pathlib
-    wikifier_cache_io_py -.-> typing
-    wikifier_cache_io_py -.-> wikifier
-    wikifier_health_impl_py -.-> hashlib
-    wikifier_health_impl_py -.-> json
-    wikifier_health_impl_py -.-> os
-    wikifier_health_impl_py -.-> re
-    wikifier_health_impl_py -.-> sys
-    wikifier_health_impl_py -.-> dataclasses
-    wikifier_health_impl_py -.-> datetime
-    wikifier_health_impl_py -.-> pathlib
-    wikifier_health_impl_py -.-> typing
-    wikifier_health_impl_py -.-> _
-    wikifier_health_pkg___init___py --> wikifier_health_impl_py
-    wikifier_mcp_server_impl_py -.-> subprocess
-    wikifier_mcp_server_impl_py -.-> re
-    wikifier_mcp_server_impl_py -.-> os
-    wikifier_mcp_server_impl_py -.-> sys
-    wikifier_mcp_server_impl_py -.-> json
-    wikifier_mcp_server_impl_py -.-> wikifier_import_cache
-    wikifier_mcp_server_impl_py -.-> time
-    wikifier_mcp_server_impl_py -.-> importlib
-    wikifier_mcp_server_impl_py -.-> argparse
-    wikifier_mcp_server_impl_py -.-> mcp_server_fastmcp
-    wikifier_mcp_server_impl_py -.-> pydantic
-    wikifier_mcp_server_impl_py -.-> pathlib
-    wikifier_mcp_server_impl_py -.-> typing
-    wikifier_mcp_server_impl_py -.-> datetime
-    wikifier_mcp_server_impl_py --> wikifier_mcp_deadline_py
-    wikifier_mcp_server_impl_py -.-> wikifier_cli
-    wikifier_mcp_server_impl_py -. ? .-> _wikifier_health_
-    wikifier_mcp_tools__common_py -.-> pathlib
-    wikifier_mcp_tools__common_py -.-> typing
-    wikifier_mcp_tools__common_py -.-> wikifier_api
-    wikifier_mcp_tools_intel_py -.-> typing
-    wikifier_mcp_tools_intel_py --> wikifier_mcp_tools__common_py
-    wikifier_mcp_tools_status_py -.-> typing
-    wikifier_mcp_tools_status_py --> wikifier_mcp_tools__common_py
-    wikifier_mcp_tools_status_py -.-> wikifier
-    wikifier_mcp_tools_workflow_py -.-> typing
-    wikifier_mcp_tools_workflow_py -.-> wikifier_api
-    wikifier_parsers_bree___init___py --> wikifier_parsers_bree__bree_py
-    wikifier_parsers_bree__bree_py -.-> json
-    wikifier_parsers_bree__bree_py -.-> re
-    wikifier_parsers_bree__bree_py -.-> warnings
-    wikifier_parsers_bree__bree_py -.-> hashlib
-    wikifier_parsers_bree__bree_py -.-> os
-    wikifier_parsers_bree__bree_py -.-> time
-    wikifier_parsers_bree__bree_py -.-> dataclasses
-    wikifier_parsers_bree__bree_py -.-> pathlib
-    wikifier_parsers_bree__bree_py -.-> typing
-    wikifier_parsers_bree__bree_py -.-> wikifier_parsers_project_root
-    wikifier_parsers_bree__bree_py -.-> wikifier_parsers_resolution
-    wikifier_parsers_bree__bree_py -.-> wikifier_resolution
-    wikifier_parsers_bree__bree_py -.-> wikifier_parsers
-    wikifier_cache__core_py -.-> json
-    wikifier_cache__core_py -.-> os
-    wikifier_cache__core_py -.-> time
-    wikifier_cache__core_py -.-> hashlib
-    wikifier_cache__core_py -.-> pathlib
-    wikifier_cache__core_py -.-> typing
-    wikifier_cache__core_py -.-> collections
-    wikifier_cache__core_py -.-> datetime
-    wikifier_cache__core_py -.-> __
-    wikifier_cache__core_py --> wikifier_contracts_py
-    wikifier_cache__core_py --> wikifier_resolution_py
-    wikifier_cache__core_py --> wikifier_cache_io_py
-    wikifier_cache__core_py --> wikifier_cache_files_py
-    wikifier_cache__core_py --> wikifier_parsers_bree___init___py
-    wikifier_cache__core_py -.-> dataclasses
-    wikifier_cache__core_py --> wikifier_project_root_py
-    wikifier_cache__core_py --> wikifier_parsers___init___py
-    wikifier_cache_acs_py --> wikifier_cache__core_py
-    wikifier_cache_barrel_py --> wikifier_cache__core_py
-    wikifier_cache_cycles_py --> wikifier_cache__core_py
-    wikifier_cache_diagnostics_py --> wikifier_cache__core_py
-    wikifier_cache_graph_py --> wikifier_cache__core_py
-    wikifier_cache_streaming_py --> wikifier_cache__core_py
-    wikifier_mcp_deadline_py -.-> os
-    wikifier_mcp_deadline_py -.-> threading
-    wikifier_mcp_deadline_py -.-> typing
-    wikifier_parsers__ldsi_py -.-> re
-    wikifier_parsers__ldsi_py -.-> typing
-    tests_test_plan_2026_08_27_py -.-> importlib
-    tests_test_plan_2026_08_27_py -.-> inspect
-    tests_test_plan_2026_08_27_py -.-> json
-    tests_test_plan_2026_08_27_py -.-> os
-    tests_test_plan_2026_08_27_py -.-> subprocess
-    tests_test_plan_2026_08_27_py -.-> sys
-    tests_test_plan_2026_08_27_py -.-> unittest
-    tests_test_plan_2026_08_27_py -.-> mcp
-    tests_test_plan_2026_08_27_py -.-> wikifier_parsers_bree
-    tests_test_plan_2026_08_27_py -.-> wikifier
-    tests_test_plan_2026_08_27_py -.-> pathlib
-    tests_test_plan_2026_08_27_py -.-> tests__base
-    tests_test_plan_2026_08_27_py -.-> wikifier_api
-    tests_test_plan_2026_08_27_py -.-> wikifier_mcp_deadline
-    tests_test_plan_2026_08_27_py -.-> wikifier_mcp_server_impl
-    tests_test_plan_2026_08_27_py -.-> wikifier_candidates
-    tests_test_plan_2026_08_27_py -.-> wikifier_health_impl
-    tests_test_plan_2026_08_27_py -.-> wikifier_parsers_javascript
-    tests_test_plan_2026_08_27_py -.-> wikifier_parsers_python
-    tests_test_plan_2026_08_27_py -. ? .-> _wikifier_health_
-    tests_test_plan_2026_08_27_py -. ? .-> _wikifier_parsers_python_
+    wikifier_serve_py -.-> _
+    tests_test_library_map_honesty_py -.-> json
+    tests_test_library_map_honesty_py -.-> re
+    tests_test_library_map_honesty_py -.-> unittest
+    tests_test_library_map_honesty_py -.-> pathlib
+    tests_test_library_map_honesty_py -.-> tests__base
+    tests_test_library_map_honesty_py -.-> wikifier_library
+    tests_test_library_map_honesty_py -.-> wikifier_agent_loop
+    tests_test_library_map_honesty_py -.-> wikifier
     tests__base_py -.-> os
     tests__base_py -.-> sys
     tests__base_py -.-> tempfile
@@ -775,6 +745,26 @@ graph TD
     tests_test_parsers_py -.-> tests__base
     tests_test_parsers_py -.-> wikifier_parsers_python
     tests_test_parsers_py -.-> wikifier_parsers_javascript
+    tests_test_plan_2026_08_27_py -.-> importlib
+    tests_test_plan_2026_08_27_py -.-> inspect
+    tests_test_plan_2026_08_27_py -.-> json
+    tests_test_plan_2026_08_27_py -.-> os
+    tests_test_plan_2026_08_27_py -.-> subprocess
+    tests_test_plan_2026_08_27_py -.-> sys
+    tests_test_plan_2026_08_27_py -.-> unittest
+    tests_test_plan_2026_08_27_py -.-> wikifier_parsers_bree
+    tests_test_plan_2026_08_27_py -.-> wikifier
+    tests_test_plan_2026_08_27_py -.-> pathlib
+    tests_test_plan_2026_08_27_py -.-> tests__base
+    tests_test_plan_2026_08_27_py -.-> wikifier_api
+    tests_test_plan_2026_08_27_py -.-> wikifier_mcp_deadline
+    tests_test_plan_2026_08_27_py -.-> wikifier_mcp_status_ops
+    tests_test_plan_2026_08_27_py -.-> wikifier_candidates
+    tests_test_plan_2026_08_27_py -.-> wikifier_health_impl
+    tests_test_plan_2026_08_27_py -.-> wikifier_parsers_javascript
+    tests_test_plan_2026_08_27_py -.-> wikifier_parsers_python
+    tests_test_plan_2026_08_27_py -. ? .-> _wikifier_health_
+    tests_test_plan_2026_08_27_py -. ? .-> _wikifier_parsers_python_
     tests_test_selftest_wrappers_py -.-> runpy
     tests_test_selftest_wrappers_py -.-> unittest
     tests_test_selftest_wrappers_py -.-> pathlib
@@ -788,7 +778,7 @@ graph TD
     tests_test_walk_coverage_resolvers_py -.-> wikifier_agent_loop
     tests_test_walk_coverage_resolvers_py -.-> wikifier_parsers
     classDef external fill:#eeeeee,stroke:#888888,stroke-dasharray: 3 3
-    class _,__,_wikifier_health_,_wikifier_import_cache_impl_,_wikifier_mcp_server_,_wikifier_parsers_python_,argparse,ast,base64,collections,contextlib,dataclasses,datetime,enum,fcntl,fnmatch,functools,hashlib,http_server,importlib,importlib_resources,inspect,io,json,mcp,mcp_server_fastmcp,modname____name__,msvcrt,name,os,pathlib,platform,pydantic,re,runpy,shutil,signal,sqlite3,subprocess,sys,tempfile,tests__base,textwrap,threading,time,traceback,typing,unittest,warnings,wikifier_agent_loop,wikifier_api,wikifier_cache,wikifier_cache_store,wikifier_candidates,wikifier_cli,wikifier_contracts,wikifier_diagnostics,wikifier_health,wikifier_health_impl,wikifier_import_cache,wikifier_library,wikifier_mcp_deadline,wikifier_mcp_server_impl,wikifier_parsers_bree,wikifier_parsers_cdia,wikifier_parsers_javascript,wikifier_parsers_python,wikifier_project_root,wikifier_resolution external
+    class _,__,__project_root,__resolution,_wikifier_health_,_wikifier_import_cache_impl_,_wikifier_mcp_server_,_wikifier_parsers_python_,argparse,ast,base64,collections,contextlib,dataclasses,datetime,enum,fcntl,fnmatch,functools,hashlib,http_server,importlib,importlib_resources,inspect,io,json,mcp,mcp_server_fastmcp,modname____name__,msvcrt,name,os,pathlib,platform,pydantic,re,runpy,shutil,signal,sqlite3,subprocess,sys,tempfile,tests__base,textwrap,threading,time,traceback,typing,unittest,warnings,wikifier,wikifier_agent_loop,wikifier_api,wikifier_cache,wikifier_cache_store,wikifier_candidates,wikifier_cli,wikifier_contracts,wikifier_diagnostics,wikifier_health,wikifier_health_impl,wikifier_import_cache,wikifier_library,wikifier_mcp_deadline,wikifier_mcp_status_ops,wikifier_parsers,wikifier_parsers_bree,wikifier_parsers_cdia,wikifier_parsers_javascript,wikifier_parsers_python,wikifier_project_root,wikifier_resolution external
 ```
 
 ## Resolved Dependencies
@@ -926,6 +916,14 @@ graph TD
 | tests/test_init_seed.py | subprocess → subprocess | medium |
 | tests/test_init_seed.py | tests._base → tests._base | medium |
 | tests/test_init_seed.py | unittest → unittest | medium |
+| tests/test_library_map_honesty.py | json → json | medium |
+| tests/test_library_map_honesty.py | pathlib → pathlib | medium |
+| tests/test_library_map_honesty.py | re → re | medium |
+| tests/test_library_map_honesty.py | tests._base → tests._base | medium |
+| tests/test_library_map_honesty.py | unittest → unittest | medium |
+| tests/test_library_map_honesty.py | wikifier → wikifier | medium |
+| tests/test_library_map_honesty.py | wikifier.agent_loop → wikifier.agent_loop | medium |
+| tests/test_library_map_honesty.py | wikifier.library → wikifier.library | medium |
 | tests/test_multi_lang_parsers.py | "wikifier.health" → "wikifier.health" | low |
 | tests/test_multi_lang_parsers.py | importlib → importlib | medium |
 | tests/test_multi_lang_parsers.py | os → os | medium |
@@ -946,7 +944,6 @@ graph TD
 | tests/test_plan_2026_08_27.py | importlib → importlib | medium |
 | tests/test_plan_2026_08_27.py | inspect → inspect | medium |
 | tests/test_plan_2026_08_27.py | json → json | medium |
-| tests/test_plan_2026_08_27.py | mcp → mcp | medium |
 | tests/test_plan_2026_08_27.py | os → os | medium |
 | tests/test_plan_2026_08_27.py | pathlib → pathlib | medium |
 | tests/test_plan_2026_08_27.py | subprocess → subprocess | medium |
@@ -958,7 +955,7 @@ graph TD
 | tests/test_plan_2026_08_27.py | wikifier.candidates → wikifier.candidates | medium |
 | tests/test_plan_2026_08_27.py | wikifier.health_impl → wikifier.health_impl | medium |
 | tests/test_plan_2026_08_27.py | wikifier.mcp.deadline → wikifier.mcp.deadline | medium |
-| tests/test_plan_2026_08_27.py | wikifier.mcp.server_impl → wikifier.mcp.server_impl | medium |
+| tests/test_plan_2026_08_27.py | wikifier.mcp.status_ops → wikifier.mcp.status_ops | medium |
 | tests/test_plan_2026_08_27.py | wikifier.parsers.bree → wikifier.parsers.bree | medium |
 | tests/test_plan_2026_08_27.py | wikifier.parsers.javascript → wikifier.parsers.javascript | medium |
 | tests/test_plan_2026_08_27.py | wikifier.parsers.python → wikifier.parsers.python | medium |
@@ -1039,7 +1036,7 @@ graph TD
 | wikifier/cache/files.py | pathlib → pathlib | medium |
 | wikifier/cache/files.py | typing → typing | medium |
 | wikifier/cache/graph.py | ._core → wikifier/cache/_core.py | high |
-| wikifier/cache/io.py | .. → wikifier | medium |
+| wikifier/cache/io.py | .. → .. | medium |
 | wikifier/cache/io.py | json → json | medium |
 | wikifier/cache/io.py | os → os | medium |
 | wikifier/cache/io.py | pathlib → pathlib | medium |
@@ -1077,7 +1074,7 @@ graph TD
 | wikifier/contracts.py | json → json | medium |
 | wikifier/contracts.py | pathlib → pathlib | medium |
 | wikifier/contracts.py | typing → typing | medium |
-| wikifier/daemon.py | . → wikifier | medium |
+| wikifier/daemon.py | . → . | medium |
 | wikifier/daemon.py | .cli → wikifier/cli.py | high |
 | wikifier/daemon.py | datetime → datetime | medium |
 | wikifier/daemon.py | json → json | medium |
@@ -1093,16 +1090,6 @@ graph TD
 | wikifier/diagnostics.py | enum → enum | medium |
 | wikifier/diagnostics.py | json → json | medium |
 | wikifier/diagnostics.py | typing → typing | medium |
-| wikifier/health.py | . → wikifier | medium |
-| wikifier/health.py | dataclasses → dataclasses | medium |
-| wikifier/health.py | datetime → datetime | medium |
-| wikifier/health.py | hashlib → hashlib | medium |
-| wikifier/health.py | json → json | medium |
-| wikifier/health.py | os → os | medium |
-| wikifier/health.py | pathlib → pathlib | medium |
-| wikifier/health.py | re → re | medium |
-| wikifier/health.py | sys → sys | medium |
-| wikifier/health.py | typing → typing | medium |
 | wikifier/health_impl.py | . → . | medium |
 | wikifier/health_impl.py | dataclasses → dataclasses | medium |
 | wikifier/health_impl.py | datetime → datetime | medium |
@@ -1137,6 +1124,7 @@ graph TD
 | wikifier/mcp/server.py | .server_impl → wikifier/mcp/server_impl.py | high |
 | wikifier/mcp/server_impl.py | "wikifier.health" → "wikifier.health" | low |
 | wikifier/mcp/server_impl.py | .deadline → wikifier/mcp/deadline.py | high |
+| wikifier/mcp/server_impl.py | .status_ops → wikifier/mcp/status_ops.py | high |
 | wikifier/mcp/server_impl.py | argparse → argparse | medium |
 | wikifier/mcp/server_impl.py | datetime → datetime | medium |
 | wikifier/mcp/server_impl.py | importlib → importlib | medium |
@@ -1152,16 +1140,15 @@ graph TD
 | wikifier/mcp/server_impl.py | typing → typing | medium |
 | wikifier/mcp/server_impl.py | wikifier.cli → wikifier.cli | medium |
 | wikifier/mcp/server_impl.py | wikifier.import_cache → wikifier.import_cache | medium |
+| wikifier/mcp/status_ops.py | "wikifier.health" → "wikifier.health" | low |
+| wikifier/mcp/status_ops.py | .deadline → wikifier/mcp/deadline.py | high |
+| wikifier/mcp/status_ops.py | importlib → importlib | medium |
+| wikifier/mcp/status_ops.py | pathlib → pathlib | medium |
+| wikifier/mcp/status_ops.py | typing → typing | medium |
+| wikifier/mcp/status_ops.py | wikifier.import_cache → wikifier.import_cache | medium |
 | wikifier/mcp/tools/_common.py | pathlib → pathlib | medium |
 | wikifier/mcp/tools/_common.py | typing → typing | medium |
 | wikifier/mcp/tools/_common.py | wikifier.api → wikifier.api | medium |
-| wikifier/mcp/tools/intel.py | ._common → wikifier/mcp/tools/_common.py | high |
-| wikifier/mcp/tools/intel.py | typing → typing | medium |
-| wikifier/mcp/tools/status.py | ._common → wikifier/mcp/tools/_common.py | high |
-| wikifier/mcp/tools/status.py | typing → typing | medium |
-| wikifier/mcp/tools/status.py | wikifier → wikifier | medium |
-| wikifier/mcp/tools/workflow.py | typing → typing | medium |
-| wikifier/mcp/tools/workflow.py | wikifier.api → wikifier.api | medium |
 | wikifier/parsers/__init__.py | importlib → importlib | medium |
 | wikifier/parsers/__init__.py | modname, __name__ → modname, __name__ | low |
 | wikifier/parsers/__init__.py | typing → typing | medium |
@@ -1170,9 +1157,9 @@ graph TD
 | wikifier/parsers/_ldsi.py | re → re | medium |
 | wikifier/parsers/_ldsi.py | typing → typing | medium |
 | wikifier/parsers/bree/__init__.py | ._bree → wikifier/parsers/bree/_bree.py | high |
-| wikifier/parsers/bree/_bree.py | .. → wikifier.parsers | medium |
-| wikifier/parsers/bree/_bree.py | ..project_root → wikifier.parsers.project_root | medium |
-| wikifier/parsers/bree/_bree.py | ..resolution → wikifier.parsers.resolution | medium |
+| wikifier/parsers/bree/_bree.py | .. → .. | medium |
+| wikifier/parsers/bree/_bree.py | ..project_root → ..project_root | medium |
+| wikifier/parsers/bree/_bree.py | ..resolution → ..resolution | medium |
 | wikifier/parsers/bree/_bree.py | dataclasses → dataclasses | medium |
 | wikifier/parsers/bree/_bree.py | hashlib → hashlib | medium |
 | wikifier/parsers/bree/_bree.py | json → json | medium |
@@ -1253,7 +1240,7 @@ graph TD
 | wikifier/resolution.py | re → re | medium |
 | wikifier/resolution.py | time → time | medium |
 | wikifier/resolution.py | typing → typing | medium |
-| wikifier/serve.py | . → wikifier | medium |
+| wikifier/serve.py | . → . | medium |
 | wikifier/serve.py | .cli → wikifier/cli.py | high |
 | wikifier/serve.py | http.server → http.server | medium |
 | wikifier/serve.py | json → json | medium |
@@ -1270,10 +1257,10 @@ graph TD
 
 ## ACS Risk Snapshot
 
-**Scored edges**: 459 | **avg_confidence**: 0.51 | **actionable_low_conf**: 42 | raw low-conf (telemetry): 397 (threshold 0.65)
+**Scored edges**: 668 | **avg_confidence**: 0.51 | **actionable_low_conf**: 58 | raw low-conf (telemetry): 578 (threshold 0.65)
 **Agent work queue**: use `actionable_low_conf_edges` + `reason_code_counts` / `agent_signal=investigate` only — do **not** thrash on raw `low_conf_edges` (includes external/bare).
-**reason_code_counts**: external_or_bare:327, high_confidence_ok:62, low_confidence_internal:42, dynamic_literal:28
-**Top risk reasons**: base:medium:368, no_resolved_path:368, base:high:62, base:low:29
+**reason_code_counts**: external_or_bare:483, high_confidence_ok:90, unresolved_project:58, dynamic_literal:37
+**Top risk reasons**: base:medium:540, no_resolved_path:540, base:high:90, base:low:38
 **Sample low-confidence edges (telemetry; prefer actionable)**:
   1. Base low (0.05). opaque dynamic expression; high complexity; conditional_dynamic semantics; creative registry_map (LDSI/CDIA); trace: ControlFlowDetector=if. Recommendation: Opaque or high-complexity dynamic resolution — refactor to static import or introduce explicit runtime guard; current edge is unsuitable for static analysis tooling.
   2. Base medium (0.48). unresolved target. Recommendation: Low-confidence or fragile edge — review the concrete usage site and consider hardening the import (or pin resolution) before trusting the dependency for automation.
@@ -1281,19 +1268,19 @@ graph TD
 
 ## Reverse Dependencies ("Who depends on me")
 
-**Targets with dependents**: 34 | **Total reverse edges**: 67
+**Targets with dependents**: 30 | **Total reverse edges**: 60
 
 **High-impact modules (most reverse dependents)**:
 - `wikifier/cache/_core.py` ← 6 files depend on it (e.g. wikifier/cache/acs.py, wikifier/cache/barrel.py, wikifier/cache/cycles.py, wikifier/cache/diagnostics.py)
 - `wikifier/contracts.py` ← 6 files depend on it (e.g. wikifier/__init__.py, wikifier/api.py, wikifier/cache/__init__.py, wikifier/cache/_core.py)
 - `wikifier/parsers/_edge.py` ← 5 files depend on it (e.g. wikifier/parsers/c_cpp.py, wikifier/parsers/csharp.py, wikifier/parsers/go_lang.py, wikifier/parsers/java.py)
-- `wikifier` ← 4 files depend on it (e.g. wikifier/cache/io.py, wikifier/daemon.py, wikifier/health.py, wikifier/serve.py)
 - `wikifier/cli.py` ← 4 files depend on it (e.g. wikifier/__init__.py, wikifier/__main__.py, wikifier/daemon.py, wikifier/serve.py)
 - `wikifier/project_root.py` ← 4 files depend on it (e.g. wikifier/agent_loop.py, wikifier/api.py, wikifier/cache/_core.py, wikifier/parsers/javascript.py)
 - `wikifier/cache/io.py` ← 3 files depend on it (e.g. wikifier/cache/__init__.py, wikifier/cache/_core.py, wikifier/cache/files.py)
 - `wikifier/resolution.py` ← 3 files depend on it (e.g. wikifier/api.py, wikifier/cache/_core.py, wikifier/parsers/javascript.py)
 - `wikifier/cache/files.py` ← 2 files depend on it (e.g. wikifier/cache/__init__.py, wikifier/cache/_core.py)
-- `wikifier/mcp/tools/_common.py` ← 2 files depend on it (e.g. wikifier/mcp/tools/intel.py, wikifier/mcp/tools/status.py)
+- `wikifier/mcp/deadline.py` ← 2 files depend on it (e.g. wikifier/mcp/server_impl.py, wikifier/mcp/status_ops.py)
+- `wikifier/parsers/__init__.py` ← 2 files depend on it (e.g. wikifier/api.py, wikifier/cache/_core.py)
 
 ## Barrel Expansions
 
@@ -1305,18 +1292,42 @@ graph TD
 
 ## Conditional & Dynamic Intelligence
 
-**Conditional imports detected**: 38
-**Dynamic imports detected**: 40
+**Conditional imports detected**: 36
+**Dynamic imports detected**: 38
 
 Sample conditional imports (fragile / feature-flagged paths):
 - `wikifier/agent_loop.py` → `"wikifier.health"`  (ctx: )
-- `wikifier/parsers/__init__.py` → `modname, __name__`  (ctx: )
-- `wikifier/mcp/server_impl.py` → `"wikifier.health"`  (ctx: )
+- `wikifier/cache/_core.py` → `import_module(" in expl or "__import__(" in expl or "importlib.import_module" in expl:
+        return True
+
+    
+    if dtype in ("static", "string", "literal"):
+        
+        i`  (ctx: )
+- `wikifier/cache/_core.py` → `__import__(" in expl or "importlib.import_module" in expl:
+        return True
+
+    
+    if dtype in ("static", "string", "literal"):
+        
+        if (raw.startswith("\"") and`  (ctx: )
 - `wikifier/mcp/server_impl.py` → `"wikifier.health"`  (ctx: )
 - `wikifier/mcp/server_impl.py` → `"wikifier.health"`  (ctx: )
 Sample dynamic imports (runtime / template-driven):
 - `wikifier/agent_loop.py` → `"wikifier.health"`  (type: static)
-- `wikifier/parsers/__init__.py` → `modname, __name__`  (type: unknown)
-- `wikifier/mcp/server_impl.py` → `"wikifier.health"`  (type: static)
+- `wikifier/cache/_core.py` → `import_module(" in expl or "__import__(" in expl or "importlib.import_module" in expl:
+        return True
+
+    
+    if dtype in ("static", "string", "literal"):
+        
+        i`  (type: expression)
+- `wikifier/cache/_core.py` → `__import__(" in expl or "importlib.import_module" in expl:
+        return True
+
+    
+    if dtype in ("static", "string", "literal"):
+        
+        if (raw.startswith("\"") and`  (type: expression)
 - `wikifier/mcp/server_impl.py` → `"wikifier.health"`  (type: static)
 - `wikifier/mcp/server_impl.py` → `"wikifier.health"`  (type: static)
diff --git a/skills/run.md b/skills/run.md
index 17d3281..e34556f 100644
--- a/skills/run.md
+++ b/skills/run.md
@@ -1,13 +1,13 @@
-# Wikifier Agent Protocol v0.6
+# Wikifier Agent Protocol v0.6.1
 
 **Formerly "Wikifier Skills & Commands". This is the authoritative, versioned specification for agent behavior when using Wikifier.**
 
-**Version**: v0.6 (v4.2.0 real-pipeline + reliability update; package current **4.6.x**, live `__version__` in `wikifier/__init__.py`)  
-**Date**: 2026-06-10 (package notes refreshed 2026-08-01; gap-closure contract 2026-07-09)  
-**Status**: Active. Supersedes v0.5.  
+**Version**: v0.6.1 (additive 4.6.x I/O notes on v0.6; package current **4.6.x**, live `__version__` in `wikifier/__init__.py`)  
+**Date**: 2026-09-11 (v0.6 dated 2026-06-10; package notes refreshed 2026-08-01; gap-closure 2026-07-09)  
+**Status**: Active. Supersedes v0.6. v0.6 agent behavior keeps working (additive fields only).  
 **See also**: `README.md`, `Findings/gap-closure-report.md`, `Findings/gap-amendment-plan-2026-08-01.md`, and the library in wikifier/.
 
-**Package 4.6.x + gap-closure notes (additive; protocol still v0.6):**
+**Package 4.6.x + gap-closure notes (additive; folded into v0.6.1):**
 - File Tree + `wikifier serve`; MCP status/attention use library + emoji (not `[GREEN]` tags).
 - **First-run:** `init` → lean `monitored_paths.txt` + `map_paths.txt` (default active root `src/`, not bare `.`) → `update-maps` → `health --summary` → `suggest_next_actions`. Map is automatic; wiki *prose* is agent-filled over time.
 - **`session_bootstrap` readiness:** message embeds the readiness tier. `blocked` is not a crash — see **§ Readiness blocked**. Hard blockers = missing map/health (or severe ghosts). Bare `.` monitor alone → `map_ok_scope_risk` when map+health exist (scope warnings / fix_scope), not the same tier as missing map. Unattended ops require **`readiness=ready_for_daemon`**, not `health_score=Map Ready` alone.
@@ -20,7 +20,7 @@
 - **Dual scope:** `monitored_paths` = check-changes/health scope (keep lean). `update-maps --directory=` / `--max-files=` = map walk. Never set `project_root` to a multi-repo parent (e.g. `cloned_sample_projects`).
 - **CLI target:** `wikifier --target /abs/project health --summary` (flags stripped before the command). Or `WIKIFIER_PROJECT_ROOT=…`.
 - **Long-horizon:** `wikifier autonomous-status` (or `readiness`) before unattended runs; daemon writes `.wikifier_staging/daemon_heartbeat.json`. Soak ≥72h is still evidence work, not automatic.
-- **Deletions:** `record-deletion` + ghost detection. **Languages:** py/js/ts/rust/go/c/c#/java (regex). journal/pending = audit queue, not Jira.
+- **Deletions:** `record-deletion` + ghost detection. **Languages:** two-tier (see table below). journal/pending = audit queue, not Jira.
 - **Huge monorepos:** lean `monitored_paths.txt` (not bare `.`). `WIKIFIER_CHECK_CHANGES_MAX` default 2000. Hygiene: `seed-health`, `prune-pending`, `prune-health`.
 - **Monitor/daemon:** mtime heartbeat; agents still own wiki/mark-green. `WIKIFIER_DAEMON_MAPS_INTERVAL` default 600s; `WIKIFIER_DAEMON_MAPS=0` for check-only.
 - Health module: `importlib.import_module("wikifier.health")` or `wikifier.health_module` — `from wikifier import health` is the *function*.
@@ -32,6 +32,21 @@
 - A POSIX lock self-deadlock in library `record_change`/`mark_green`/`check_changes` was fixed (locking is now re-entrant per process). MCP timeouts on those tools should no longer occur; the CLI fallback guidance below remains valid as defense in depth.
 - A stdlib-only test suite exists: `python -m unittest discover tests` (run it when working on Wikifier itself).
 
+**v0.6.1 migration notes (package 4.6.x; additive on v0.6)** — no mandatory I/O break; tolerate new keys:
+- **Readiness tiers** (`session_bootstrap.readiness`): `blocked` / `map_ok_scope_risk` / `ready_for_daemon` / `ready_with_agent_wiki_work` / `not_ready`. Unattended work needs `ready_for_daemon`, not `health_score=Map Ready` alone.
+- **`map_paths.txt` vs `monitored_paths.txt`:** map package roots vs wiki/health watch. Independent. Wiki-only monitor lists do **not** define the map.
+- **ACS v1.3:** `actionable_low_conf_edges`, `reason_code_counts`, `agent_signal` (`skip`|`investigate`). Never thrash on raw `low_conf_edges`.
+- **Index-first maps:** `index_first_dirty` / `candidates_reused` on `update_maps`. `success: true` ≠ map complete — use `map_coverage.complete`.
+- **`record_change`:** additive `needs_mark_green: true`; stays Yellow until `mark_green`.
+- **`session_bootstrap` cache fields:** `cache_backend` is `sqlite` | `sqlite+json` | `json` | `none`. **`none` means no sqlite/json file at read time.** An empty SQLite file (schema only, `files` table count = 0) is still `sqlite`, not `none`. Additive `cache_empty` (bool) and `cache_files_indexed` (int) make that split explicit. ACS zeros + `cache_empty: true` means “no pairs yet”, not “no backend”. `cache-status` reports the file backend; bootstrap used to leave `cache_backend: "none"` after creating the empty stub — that is fixed; do not equate the two tools without checking `cache_empty`.
+- **Committed `library.md`:** regenerate with `update-maps`; do not hand-edit. Nodes must be files on disk.
+- **Language depth (G9):** deep/ACS = Python + JS/TS; Rust/Go/C/C++/C#/Java are regex hints.
+
+| Depth | Languages | Trust |
+|-------|-----------|--------|
+| Deep / ACS | Python, JS/TS | CDIA, BREE, scored resolve, ACS work queue |
+| Regex hint | Rust, Go, C/C++, C#, Java | `use`/`import`/`#include`/`using` smokes — not cargo/`go.mod`/classpath/`-I` |
+
 **Core design**: Token-efficient agent-to-agent wiki. Agents use it to look up files (health matrix + file wikis + BRC + stele chunks instead of full sources), autonomously update wiki summaries, and create new ones as work progresses. **It should not be used for anything more than that.** 
 
 This protocol + the Python package + MCP server form the bridge for consistent, low-ambiguity agent operation on real external projects.
@@ -140,7 +155,7 @@ See also: Findings note `Findings/readiness-blocked-bare-monitor-2026-07.md`.
 **Copy this exact block into the system prompt or the very first instruction of every new LLM session that uses Wikifier:**
 
 ```
-You are now operating inside a Wikifier-managed codebase (Agent Protocol v0.6 — package 4.6.x).
+You are now operating inside a Wikifier-managed codebase (Agent Protocol v0.6.1 — package 4.6.x).
 
 This is strictly an agent-to-agent wiki for token saving: map lookup (health + file wikis + deps) instead of full sources; selective wiki updates; not a human docs product or Jira.
 
diff --git a/tests/test_library_map_honesty.py b/tests/test_library_map_honesty.py
new file mode 100644
index 0000000..27b39d7
--- /dev/null
+++ b/tests/test_library_map_honesty.py
@@ -0,0 +1,195 @@
+"""library.md must name only files that exist on disk.
+
+Drives the shipped generator and the committed dogfood artifact — not mocks.
+"""
+from __future__ import annotations
+
+import json
+import re
+import unittest
+from pathlib import Path
+
+from tests._base import REPO_ROOT, TempProjectTestCase
+from wikifier.library import generate_library_md
+
+# 4.6.10 leftovers that must not reappear in the committed map.
+GONE_PATHS = (
+    "wikifier/mcp/tools/intel.py",
+    "wikifier/mcp/tools/status.py",
+    "wikifier/mcp/tools/workflow.py",
+    "wikifier/parsers/javascript/_parser.py",
+    "wikifier/parsers/javascript/__init__.py",
+    "wikifier/health.py",
+    "wikifier/mcp/server_backup.py",
+    "wikifier/parsers/bree.py",
+)
+
+GONE_MERMAID_IDS = (
+    "wikifier_mcp_tools_intel_py",
+    "wikifier_mcp_tools_status_py",
+    "wikifier_mcp_tools_workflow_py",
+    "wikifier_parsers_javascript__parser_py",
+    "wikifier_health_py",
+    "wikifier_mcp_server_backup_py",
+    "wikifier_parsers_bree_py",
+)
+
+# Project-relative source paths as they appear in tables / reverse-deps / prose.
+_REL_PATH_RE = re.compile(
+    r"(?:`)?((?:wikifier|tests|skills|Findings|docs|\.github)"
+    r"/[A-Za-z0-9_./+-]+\.[A-Za-z0-9.]+)"
+)
+
+
+def _parse_file_tree_paths(text: str):
+    """Reconstruct project-relative paths from the File Tree fence."""
+    m = re.search(r"## File Tree.*?```text\n(.*?)```", text, re.S)
+    if not m:
+        return []
+    paths = []
+    stack = []  # (depth, dir_name)
+    for line in m.group(1).splitlines():
+        if not line.strip() or line.startswith("…"):
+            continue
+        if re.match(r"^[^│├└].*/\s+\(\d+ files\)\s*$", line):
+            continue
+        mm = re.match(r"^([ │]*)(?:├── |└── )(.+)$", line)
+        if not mm:
+            continue
+        prefix, rest = mm.groups()
+        depth = len(prefix) // 4
+        name = rest.split(" — ", 1)[0].strip()
+        if name.startswith("…"):
+            continue
+        name = re.sub(r"\s+\(\d+ files\)\s*$", "", name)
+        while stack and stack[-1][0] >= depth:
+            stack.pop()
+        if name.endswith("/"):
+            stack.append((depth, name.rstrip("/")))
+            continue
+        parts = [d[1] for d in stack] + [name]
+        paths.append("/".join(parts))
+    return paths
+
+
+def _named_rel_paths(text: str):
+    found = set(_parse_file_tree_paths(text))
+    for m in _REL_PATH_RE.finditer(text):
+        found.add(m.group(1).rstrip("`"))
+    return sorted(found)
+
+
+class TestGenerateLibraryOmitsMissingFiles(TempProjectTestCase):
+    def test_generate_library_md_omits_missing_cache_keys(self):
+        self.write("pkg/live.py", "import os\n")
+        cache = {
+            "pkg/live.py": {
+                "mtime": 1,
+                "resolved_pairs": [{
+                    "raw": "os",
+                    "resolved": "",
+                    "confidence": "medium",
+                }],
+            },
+            "pkg/gone.py": {
+                "mtime": 1,
+                "resolved_pairs": [{
+                    "raw": "./helper",
+                    "resolved": "pkg/helper.py",
+                    "confidence": "high",
+                }],
+            },
+            "_reverse_dependencies": {
+                "pkg/helper.py": ["pkg/gone.py", "pkg/live.py"],
+                "pkg/live.py": ["pkg/gone.py"],
+            },
+        }
+        md = generate_library_md(self.root, cache)
+        self.assertIn("live.py", md)
+        self.assertNotIn("gone.py", md)
+        self.assertNotIn("helper.py", md)
+        self.assertNotIn("pkg/gone.py", md)
+        self.assertNotIn("pkg/helper.py", md)
+
+    def test_file_tree_prefers_wiki_not_health_reason(self):
+        self.write("pkg/mod.py", "x = 1\n")
+        self.write(
+            "pkg/mod.py.wiki.md",
+            "# pkg/mod.py\n\n## Purpose\n\nImport parser helper.\n",
+        )
+        health = {
+            "entries": {
+                "pkg/mod.py": {
+                    "status": "🟢 Green",
+                    "reason": "4.6.13 plan aligned",
+                }
+            }
+        }
+        (self.root / "file_health.json").write_text(
+            json.dumps(health), encoding="utf-8"
+        )
+        cache = {"pkg/mod.py": {"mtime": 1, "resolved_pairs": []}}
+        md = generate_library_md(self.root, cache)
+        self.assertIn("Import parser helper", md)
+        self.assertNotIn("plan aligned", md)
+
+    def test_wiki_role_colon_inside_bold(self):
+        self.write("pkg/mod.py", "x = 1\n")
+        self.write(
+            "pkg/mod.py.wiki.md",
+            "# pkg/mod.py\n\n**Role:** Gap-closure regressions.\n",
+        )
+        md = generate_library_md(
+            self.root, {"pkg/mod.py": {"mtime": 1, "resolved_pairs": []}}
+        )
+        self.assertIn("Gap-closure regressions.", md)
+        self.assertNotIn("Role:**", md)
+
+
+class TestCommittedLibraryMdMatchesTree(unittest.TestCase):
+    def test_library_md_paths_exist_on_disk(self):
+        lib = REPO_ROOT / "library.md"
+        self.assertTrue(lib.is_file(), "committed library.md missing")
+        text = lib.read_text(encoding="utf-8")
+        missing = []
+        for rel in _named_rel_paths(text):
+            if not (REPO_ROOT / rel).is_file():
+                missing.append(rel)
+        self.assertEqual(
+            missing,
+            [],
+            "library.md names paths that are not files on disk: {0}".format(
+                missing[:20]
+            ),
+        )
+
+    def test_library_md_omits_deleted_4_6_10_leftovers(self):
+        text = (REPO_ROOT / "library.md").read_text(encoding="utf-8")
+        present = [p for p in GONE_PATHS if p in text]
+        self.assertEqual(present, [], present)
+        ids = [i for i in GONE_MERMAID_IDS if i in text]
+        self.assertEqual(ids, [], ids)
+
+
+class TestBootstrapCacheBackendHonesty(TempProjectTestCase):
+    def test_empty_sqlite_is_not_cache_backend_none(self):
+        from wikifier.agent_loop import session_bootstrap
+        from wikifier import cache_store as cs
+
+        boot = session_bootstrap(project_root=self.root)
+        self.assertTrue(boot.get("success"), boot)
+        self.assertIn("cache_empty", boot)
+        self.assertIn("cache_files_indexed", boot)
+        if cs.has_sqlite(self.root) or cs.json_path(self.root).is_file():
+            self.assertNotEqual(
+                boot.get("cache_backend"),
+                "none",
+                "empty sqlite/json store must not report cache_backend=none",
+            )
+        if boot.get("cache_backend") == "none":
+            self.assertTrue(boot.get("cache_empty"))
+            self.assertEqual(boot.get("cache_files_indexed"), 0)
+
+
+if __name__ == "__main__":
+    unittest.main()
diff --git a/wikifier/agent_loop.py b/wikifier/agent_loop.py
index a4c4c26..3c8e690 100644
--- a/wikifier/agent_loop.py
+++ b/wikifier/agent_loop.py
@@ -648,8 +648,18 @@ def session_bootstrap(
             cache = ic.load_cache(root) or {}
             acs = ic.ensure_acs_summary_persisted(cache, root) or {}
             cyc = cache.get("_cycles") or {}
-            if cs is not None and not out.get("cache_backend"):
+            # Re-read after persist: creating an empty sqlite must not leave "none".
+            if cs is not None:
                 out["cache_backend"] = cs.backend_name(root)
+        try:
+            n = 0
+            if cs is not None:
+                n = len(cs.load_mtime_index(root) or {})
+            out["cache_files_indexed"] = n
+            out["cache_empty"] = n == 0
+        except Exception:
+            out.setdefault("cache_files_indexed", 0)
+            out.setdefault("cache_empty", True)
         acs_actionable = int(acs.get("actionable_low_conf_edges") or 0)
         out["acs"] = {
             "acs_version": acs.get("acs_version"),
diff --git a/wikifier/library.py b/wikifier/library.py
index 3703ab7..f248356 100644
--- a/wikifier/library.py
+++ b/wikifier/library.py
@@ -507,41 +507,95 @@ def _generate_conditional_dynamic_section(cache: Dict[str, Any]) -> List[str]:
 
 
 # ---------------------------------------------------------------------------
-# Public API
+# Live-path filter (stale cache keys must not become map nodes)
 # ---------------------------------------------------------------------------
 
-# ---------------------------------------------------------------------------
-# File tree (the primary human/agent view of project shape)
-# ---------------------------------------------------------------------------
+_SOURCE_SUFFIXES = (
+    ".py", ".js", ".ts", ".tsx", ".jsx", ".mjs", ".cjs", ".mts", ".cts",
+    ".go", ".rs", ".c", ".h", ".cpp", ".cc", ".cxx", ".hpp", ".hh",
+    ".cs", ".java", ".md", ".sh",
+)
 
-def _clean_reason(reason: str) -> Optional[str]:
-    """Normalise a health reason into a short description, or None for
-    auto-yellow boilerplate (it describes the tracking system, not the file)."""
-    reason = re.sub(r"\s+", " ", str(reason or "")).strip()
-    if not reason or reason.startswith("mtime changed") or "auto-detected" in reason:
-        return None
-    return (reason[:90] + "…") if len(reason) > 91 else reason
 
+def _is_live_file(root: Path, rel: str) -> bool:
+    rel = str(rel or "").replace("\\", "/").strip()
+    if not rel or rel.startswith("_") or "\n" in rel:
+        return False
+    try:
+        return Path(root, rel).is_file()
+    except (OSError, ValueError):
+        return False
 
-def _load_health_descriptions(root: Path) -> Dict[str, str]:
-    """file -> short description, from file_health.json or file_health.md.
 
-    Projects maintained through the shell workflow only have the .md table
-    (the JSON is written by the Python health module), so both are read.
+def _looks_like_rel_file(rel: str) -> bool:
+    rel = str(rel or "").replace("\\", "/").strip()
+    if not rel or rel.startswith("_"):
+        return False
+    lower = rel.lower()
+    return ("/" in rel) or lower.endswith(_SOURCE_SUFFIXES)
+
+
+def _wiki_caption(root: Path, rel: str) -> Optional[str]:
+    """Short purpose/role line from ``{rel}.wiki.md``, or None.
+
+    Health *reasons* are audit stamps and must not be used as captions.
     """
-    desc: Dict[str, str] = {}
+    wiki = Path(root, rel + ".wiki.md")
+    if not wiki.is_file():
+        return None
+    try:
+        text = wiki.read_text(encoding="utf-8", errors="replace")
+    except OSError:
+        return None
+    lines = text.splitlines()
+    picked = None
+    heading_re = re.compile(r"^#{1,6}\s+(purpose|role)\b", re.I)
+    role_re = re.compile(r"^\*\*role:?\*\*\s*(.*)$", re.I)
+    for i, line in enumerate(lines):
+        s = line.strip()
+        if heading_re.match(s):
+            for nxt in lines[i + 1:]:
+                n = nxt.strip()
+                if not n:
+                    continue
+                if n.startswith("#"):
+                    break
+                picked = n.lstrip("-* ").strip()
+                break
+            if picked:
+                break
+        m2 = role_re.match(s)
+        if m2 and m2.group(1).strip():
+            picked = m2.group(1).strip()
+            break
+    if not picked:
+        for line in lines:
+            s = line.strip()
+            if not s or s.startswith("#") or s.startswith(">") or s.startswith("|"):
+                continue
+            picked = s.lstrip("-* ").strip()
+            break
+    if not picked:
+        return None
+    picked = re.sub(r"\s+", " ", picked)
+    return (picked[:90] + "…") if len(picked) > 91 else picked
+
+
+def _health_tracked_files(root: Path) -> List[str]:
+    """On-disk files listed in the health matrix (keys only; reasons ignored)."""
+    tracked: List[str] = []
     try:
         with open(root / "file_health.json", "r", encoding="utf-8") as f:
             data = json.load(f)
         entries = data.get("entries", data) if isinstance(data, dict) else {}
-        for file, e in entries.items():
-            r = _clean_reason((e or {}).get("reason"))
-            if r:
-                desc[str(file)] = r
+        for file in entries:
+            k2 = str(file).rstrip("/")
+            if k2 and _is_live_file(root, k2):
+                tracked.append(k2)
     except Exception:
         pass
-    if desc:
-        return desc
+    if tracked:
+        return tracked
     try:  # .md fallback: | File | Status | Last Updated | Reason / Intent |
         with open(root / "file_health.md", "r", encoding="utf-8") as f:
             for line in f:
@@ -550,12 +604,69 @@ def _load_health_descriptions(root: Path) -> Dict[str, str]:
                     continue
                 parts = [p.strip() for p in line.split("|")]
                 if len(parts) >= 6 and parts[1]:
-                    r = _clean_reason(parts[4])
-                    if r:
-                        desc[parts[1]] = r
+                    k2 = parts[1].rstrip("/")
+                    if k2 and _is_live_file(root, k2):
+                        tracked.append(k2)
     except Exception:
         pass
-    return desc
+    return tracked
+
+
+def _live_cache_view(root: Path, cache: Dict[str, Any]) -> Dict[str, Any]:
+    """Shallow copy dropping per-file entries whose source is missing on disk."""
+    if not isinstance(cache, dict):
+        return {}
+    out: Dict[str, Any] = {}
+    for k, v in cache.items():
+        if not isinstance(k, str):
+            continue
+        if k.startswith("_"):
+            out[k] = v
+            continue
+        if _is_live_file(root, k):
+            out[k] = v
+    rev = out.get("_reverse_dependencies")
+    if isinstance(rev, dict):
+        new_rev: Dict[str, List[str]] = {}
+        for tgt, srcs in rev.items():
+            tgt_s = str(tgt)
+            if _looks_like_rel_file(tgt_s) and not _is_live_file(root, tgt_s):
+                continue
+            if not isinstance(srcs, list):
+                continue
+            live_srcs = []
+            for s in srcs:
+                ss = str(s)
+                if _looks_like_rel_file(ss) and not _is_live_file(root, ss):
+                    continue
+                live_srcs.append(ss)
+            if live_srcs:
+                new_rev[tgt_s] = live_srcs
+        out["_reverse_dependencies"] = new_rev
+    return out
+
+
+def _filter_live_edges(
+    root: Path, edges: List[Tuple[str, str, str, str, bool]]
+) -> List[Tuple[str, str, str, str, bool]]:
+    """Drop edges whose source (or resolved internal target) is not on disk."""
+    out = []
+    for src, raw, target, conf, internal in edges:
+        if _looks_like_rel_file(src) and not _is_live_file(root, src):
+            continue
+        if internal and _looks_like_rel_file(target) and not _is_live_file(root, target):
+            continue
+        out.append((src, raw, target, conf, internal))
+    return out
+
+
+# ---------------------------------------------------------------------------
+# Public API
+# ---------------------------------------------------------------------------
+
+# ---------------------------------------------------------------------------
+# File tree (the primary human/agent view of project shape)
+# ---------------------------------------------------------------------------
 
 
 TREE_DIR_FILE_CAP = 40      # files listed per directory before "… +N more"
@@ -574,21 +685,12 @@ def _generate_tree_section(root: Path, cache: Dict[str, Any]) -> List[str]:
         │   └── python.py
         └── cli.py — entry point + full update pipeline
     """
-    descriptions = _load_health_descriptions(root)
-    parsed = {k for k in cache.keys() if isinstance(k, str) and not k.startswith("_")}
-    # Health keys are free text (audit records may use whole sentences as the
-    # "file"; some entries point at directories): only real on-disk files —
-    # or parser-confirmed ones — belong in the tree.
-    tracked = set()
-    for k in descriptions:
-        k2 = k.rstrip("/")
-        if not k2 or k2 in parsed:
-            continue
-        try:
-            if (root / k2).is_file():
-                tracked.add(k2)
-        except OSError:
-            continue
+    parsed = {
+        k for k in cache.keys()
+        if isinstance(k, str) and not k.startswith("_") and _is_live_file(root, k)
+    }
+    # Health keys may be sentences or directories; only live files belong here.
+    tracked = {k for k in _health_tracked_files(root) if k not in parsed}
     files = sorted(parsed | tracked)
     if not files:
         return ["## File Tree", "", "```text",
@@ -632,15 +734,16 @@ def render(node: Dict[str, Any], prefix: str, path_prefix: str) -> None:
                 out.append(prefix + connector + name + suffix)
                 render(sub, child_prefix, path_prefix + name)
             else:
-                d = descriptions.get(path_prefix + name)
+                d = _wiki_caption(root, path_prefix + name)
                 out.append(prefix + connector + name + ((" — " + d) if d else ""))
 
     render(tree, "", "")
 
     lines = [
         "## File Tree", "",
-        "> Every parsed/tracked file, organised by folder. Descriptions come from",
-        "> the agent wiki (file_health). The dependency graph is further below.",
+        "> Every parsed/tracked file, organised by folder. Captions come from",
+        "> `*.wiki.md` purpose/role text when present. Health *reasons* are audit",
+        "> stamps and are not copied here. The dependency graph is further below.",
         "", "```text",
         "{0}/  ({1} files)".format(root.name, len(files)),
     ]
@@ -655,7 +758,8 @@ def generate_library_md(root: Path, cache: Dict[str, Any]) -> str:
     """Render library.md content from an import cache (see module docstring)."""
     if not isinstance(cache, dict):
         cache = {}
-    edges = _collect_edges(cache)
+    cache = _live_cache_view(root, cache)
+    edges = _filter_live_edges(root, _collect_edges(cache))
 
     lines = [
         "# Library & Imports Map (auto-generated by wikifier update-maps)",
@@ -702,8 +806,9 @@ def write_library_md(root: Path, cache: Optional[Dict[str, Any]] = None) -> Dict
             cache = load_cache(root)
         if not isinstance(cache, dict):
             cache = {}
-        content = generate_library_md(root, cache)
-        nodes, edges = _graph_stats(cache)
+        live = _live_cache_view(root, cache)
+        content = generate_library_md(root, live)
+        nodes, edges = _graph_stats(live)
         tmp_path = out_path.with_name(out_path.name + ".tmp")
         tmp_path.write_text(content, encoding="utf-8")
         os.replace(str(tmp_path), str(out_path))
diff --git a/wikifier/library.py.wiki.md b/wikifier/library.py.wiki.md
new file mode 100644
index 0000000..514667f
--- /dev/null
+++ b/wikifier/library.py.wiki.md
@@ -0,0 +1,7 @@
+# wikifier/library.py
+
+**Role**: Pure-Python generator for committed `library.md` (file tree, Mermaid, tables, ACS, reverse deps).
+
+## Purpose
+
+Render the import map from the cache. Omit cache keys whose source is missing on disk. File-tree captions come from `*.wiki.md` purpose/role text, never health audit reasons. Regenerated by `update-maps`; do not hand-edit `library.md`.