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

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.

Signed-off-by: Clément Deust <clement.deust@gmail.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

src/cli/cli.c

@@ -1513,8 +1513,8 @@ static const char skill_content[] =
     "\n"
     "## Edge Types\n"
     "CALLS, HTTP_CALLS, ASYNC_CALLS, DATA_FLOWS, IMPORTS, DEFINES, DEFINES_METHOD,\n"
-    "HANDLES, IMPLEMENTS, OVERRIDE, USAGE, CALL_REFERENCE, CONFIGURES, FILE_CHANGES_WITH,\n"
-    "SIMILAR_TO, SEMANTICALLY_RELATED, CONTAINS_FILE, CONTAINS_FOLDER,\n"
+    "HANDLES, IMPLEMENTS, OVERRIDE, USAGE, CALL_REFERENCE, CONFIGURES, REFERENCES_FILE,\n"
+    "FILE_CHANGES_WITH, SIMILAR_TO, SEMANTICALLY_RELATED, CONTAINS_FILE, CONTAINS_FOLDER,\n"
     "CONTAINS_PACKAGE\n"
     "\n"
     "## Cypher Examples (for query_graph)\n"