[HaoZeke]

Page open pull requests and changed files

examples/easyconfigs-pr-overlap/fetch-prs.sh and examples/eessi-pr-overlap/fetch-prs.sh read open pull requests and changed files one page at a time.

What was wrong

Both scripts passed the open-list URL and the changed-file URL to one gh api --paginate call.
The changed-file call exits non-zero when GitHub answers 422 at its cap of 3000 files.
The scripts kept the filenames already printed and did not record that the list was cut, so a capped pull request was treated as a complete file list.
The tests used 102 open pull requests, so a walk that stopped at 500 still passed.

What changed

Each script requests pages of 100 itself.

• Open pull requests continue until a page is short.
  The walk does not stop at 500.
• Changed files continue until a page is short.
  After 3000 names, one further page is probed.
  HTTP 422 that names the cap, or another non-empty page, sets file_list_truncated.
  Names past 3000 are not kept.
  The pull request is still written.
  pr-overlap notes truncated at GitHub's limit.
• Each script names the page size (page_size=100), the file cap (file_cap=3000, also used in the 422 message match), and the page limits (open_page_limit=1000, file_page_limit=40) at the top.

Before and after

Before, the fixture stopped short of pull request 501 (page 6 of a 100-wide list).
A file list that hit the cap left no file_list_truncated flag.

After, a fixture of 501 open pull requests prints open pull requests: 501 and writes prs/501.json for the pull request that changes an easyconfig or a 2026.06 easystack.
A changed file at position 501 (page 6) is kept, with no truncation flag.
A list that answers 422 on the page after 3000 files exits 0, keeps the pull request, and sets file_list_truncated to true.

Tests

cargo +stable fmt --all --check exited 0.
cargo +stable clippy --locked --all-targets -- -D warnings exited 0.
cargo +stable test --locked --all-targets exited 0.
cargo +stable test --locked --test fetch_prs_script was 10 passed, 0 failed.
shellcheck on both scripts exited 0.

Reproduce

cargo +stable test --locked --test fetch_prs_script \
  easyconfigs_fetch_reads_open_pull_requests_past_five_hundred \
  eessi_fetch_reads_open_pull_requests_past_five_hundred \
  easyconfigs_fetch_pages_files_past_five_hundred_and_keeps_the_cap \
  eessi_fetch_pages_files_past_five_hundred_and_keeps_the_cap

---

Note

Medium Risk
Changes build-order graph walking and source-probe classification; PR-fetch scripts alter which PRs and file lists downstream overlap sees when repos are large or capped.

Overview
Adds stack order --installed (and eb_stack_order installed) so build orders skip modules already on the site—using the same module list/Lmod inventory as stack gap --installed—and omit dependencies that were installed with them. --filter-deps still runs first; stdout reports installed=N before order=.

Reworks examples/easyconfigs-pr-overlap/fetch-prs.sh and examples/eessi-pr-overlap/fetch-prs.sh to page open PRs and changed files 100 at a time (no 500 stop). When GitHub caps a PR at 3000 files, the PR JSON is still written with file_list_truncated, with tests for 501 open PRs and deep file lists.

stack arch --probe-sources with two --arch values now compares only that pair (arch-missing vs unreachable); docs and tests cover the Kaleido fixture.

Expands MCP/README/CHANGELOG with a 51-tool command↔tool table in mcp.org and a test that every CLI subcommand (and listed tool name) appears there.

^{Reviewed by Cursor Bugbot for commit 9be50b1. Bugbot is set up for automated code reviews on this repo. Configure here.}