feat(config): surface matches hidden by extension filters

[reneleonhardt]

What does this PR do?

• Make MCP file searches respect the project's only and exclude filters.
• Apply those filters consistently to context, structure, project-statistics, dependency, and file-graph scans.
• When only hides real matches, report them and explain how to include or suppress their extensions.
• Enable extension hints by default with guidance.missing_extension_hints; set it to false to disable them.
• Allow selected hints to be suppressed with guidance.ignored_extensions.

Type of change

• Bug fix
• New feature
• New language support
• Documentation
• Other (describe below)

Checklist

• I've tested this locally with go build && ./codemap .
• I've read CONTRIBUTING.md (for new language support)
• I've updated documentation if needed

Additional notes

Repository languages evolve after initial setup. Actionable misses prevent agents from repeatedly failing or silently falling back to raw filesystem searches, without rescanning or changing config automatically.

Focused MCP, context, dependency, and file-graph tests pass with the full race
suite, formatting, module verification, vet, staticcheck, and a built-binary
parity probe. The probe confirmed the CLI context, MCP structure, and MCP project
statistics all report the same configured file count.

Reviewer setup:

set -euo pipefail

ROOT=$PWD
BRANCH=feat/config-only-fallback
REVIEW_ROOT=$(mktemp -d "${TMPDIR:-/tmp}/codemap-config-fallback.XXXXXX")
WT="$REVIEW_ROOT/worktree"
DEBUG_BIN="$REVIEW_ROOT/codemap-debug"
COVERAGE_OUT="$REVIEW_ROOT/coverage.out"

git worktree add --detach "$WT" "$BRANCH"

cleanup() {
  cd "$ROOT"
  git worktree remove --force "$WT"
  rm -rf "$REVIEW_ROOT"
}
trap cleanup EXIT

cd "$WT"
go fmt ./...
git diff --exit-code
go mod verify
go vet ./...
staticcheck ./...
go test -race -coverprofile="$COVERAGE_OUT" ./...
go build -gcflags='all=-N -l' -o "$DEBUG_BIN" .
"$DEBUG_BIN" .
cleanup
trap - EXIT

Developed with carefully directed, manually reviewed AI assistance. Allow edits by maintainers is enabled, so maintainers are welcome to fix wording or make minor cleanup directly; broader review feedback will be incorporated.

Co-Authored-By: GPT-5.6 Sol codex@openai.com