feat(pipeline): link markdown file references into the graph

[cdeust]

Markdown docs reference other repo files constantly (a coding-standards doc links the modules it governs, a README points at entry points) but none of that surfaced as edges, so fan-in queries were blind to documentation hubs. In an A/B retrieval benchmark I ran in August on a docs-heavy repo, the graph's top fan-in answer was off by roughly 17x: the most-referenced file was a standards doc with 173 references and zero inbound edges.

New pre-dump pass, pass_doclinks.c, modeled on pass_configlink.c: three strategies emit REFERENCES_FILE edges between existing File nodes only (unresolvable targets are dropped, the pass never invents nodes): inline links, backtick paths, bare path mentions. Targets resolve against the referencing file's directory and the repo root; repeated references collapse into one edge carrying strategy, confidence and count. Registered in the pre-dump sequence after configlink and in the incremental post-passes; REFERENCES_FILE added to the skill's edge-type list and the structural/language contract tests.

Tests mirror test_configlink.c (real files in a tmpdir, File nodes in a gbuf, run the pass, assert edges): inline link, backtick, bare mention, http/anchor ignored, anchor-suffixed file link, dedupe with count, relative-vs-root resolution, unresolvable-target guard, NULL repo_path skip.

A companion change adds the same linking for shell files (source lines and script invocations); split out to keep each change reviewable.

Validation: scripts/build.sh clean; focused serial runner (doclinks, configlink, pipeline, edge_structural, lang_contract) 340 passed under ASan/UBSan; cppcheck clean on the new files with the repo's flags.

Claude-Session: https://claude.ai/code/session_017cfk6PdDBWPmrzZksULGhD

What does this PR do?

Checklist

• Every commit is signed off (git commit -s) — required, CI rejects
  unsigned commits (DCO, see CONTRIBUTING.md)
• Tests pass locally (make -f Makefile.cbm test)
• Lint passes (make -f Makefile.cbm lint-ci)
• New behavior is covered by a test (reproduce-first for bug fixes)

[github-actions]

Thanks for opening this — it has been seen, and it is queued.

This note is automated, but it is not a brush-off: it exists so you know where your PR stands instead of having to guess from silence.

Current review status: working through a backlog. 0.9.1-rc.1 is out, so the release freeze that held reviews is over — but it left a large queue of open pull requests behind it, and we are reading through them oldest-first. The background is in discussion #1144.

What that means for this PR, concretely:

• It will not be closed for inactivity. No stale bot touches pull requests here.
• It may still sit a while before a human reads it. That is on us, not on you.
• Older PRs are read first, so a recent one is not being skipped — it is behind a queue.

Things that will genuinely speed it up whenever review does happen:

• Keep it rebased on main — the tree is moving quickly right now, and a conflicting branch cannot be reviewed as the diff you intended.
• Get CI green, or say which failures you believe are pre-existing.
• Keep the change to one claim. Bundled features and refactors get split before they get merged, which costs you a round trip.
• Every commit needs a sign-off (git commit -s) — CI enforces DCO.

If this fixes a bug, a reproduction we can run is worth more than a description of the symptom.

Thanks for contributing, and sorry in advance for the wait.