fix(cache): re-anchor CWD-relative source_file on write so warm hits keep canonical symbol ids

[rajarshidattapy]

Fixes #2630.

Not an astro defect

extract_astro()'s ID recipe is already correct — a cold run produces exactly what
the issue asks for:

pages_index          # file node
pages_index_posts    # frontmatter variable -- correctly prefixed

Both reported symptoms only appear on a warm AST cache hit, and the cause is a
round-trip asymmetry in graphify/cache.py:

• Extractors stamp source_file with the path string extract() was handed, so a
  relative input yields a CWD-relative stamp (src/pages/index.astro).
• _relativize_source_files_in skipped relative values on write ("already-relative
  fields pass through unchanged"), but _absolutize_source_files_in reads them back as
  root-relative (root / sp).
• When CWD is not the inferred root the two disagree, and a warm hit resurrects
  <root>/src/pages/index.astro — a path that names no file.

Every source_file-gated remap in extract() then misses. The one that matters here
is the file-stem prefix pass, which looks up Path(source_file).resolve() in
prefix_remap (extract.py:5756); with the lookup broken, the symbol keeps the
raw-input-path stem that a cold run rewrites. Hence src_pages_index_posts (case 1), and
for absolute inputs the on-disk path survives into the persisted id (case 2's leak class).

Astro only looks special

.astro is cached; .js/.jsx/.mjs/.cjs/.ts/.tsx/.mts/.cts/.vue/.svelte are all in
_JS_CACHE_BYPASS_SUFFIXES and never round-trip through the cache. That is the entire
reason the report's content.ts node stayed correct while its .astro sibling did not.
The defect is language-agnostic — Python reproduces it identically:

run 1 (cold)   lib_content_get_posts
run 2 (warm)   src_lib_content_get_posts

Fix

One place, upstream of every extractor: the write side re-anchors a CWD-relative
source_file to root-relative, so _absolutize_source_files_in becomes a true inverse.

Guarded to fail closed — it rewrites only when the CWD-relative reading names a real file
and differs from the root-relative reading. A fragment that already stores
root-relative (a semantic subagent's, per _normalize_source_file_value) and a ghost path
are both left exactly as before.

What is deliberately not changed

• extract_astro() — nothing to fix, and the issue's suggested post-pass
  assert sym_id.startswith(file_stem + "_") is redundant once the shared gate is correct.
  An assert would also turn a stale cache entry into a crash.
• Cross-root shared cache_root — extract(sub, cache_root=X) after
  extract(super, cache_root=X) still replays a stale rel path, because the
  $graphify-root$ marker (AST cache replays node ids minted under the original root after a corpus move/clone #2257) re-anchors only the root portion and assumes a file's
  path within the root is unchanged. Separate design limit, and not reachable from this
  issue's repro (default cache_root follows root).

Verification

scenario	before	after
case 1 warm (relative inputs, CWD above root)	src_pages_index_posts	pages_index_posts
case 2 (absolute single-file input)	index_posts / leaked slug when warmed cross-root	index_posts
python equivalent, warm	src_lib_content_get_posts	lib_content_get_posts

New test tests/test_cache.py::test_warm_hit_with_relative_inputs_from_above_the_root
asserts warm ids == cold ids and that every symbol sits under its file node's stem. It
carries the same warmth probe as the #2257 test, so a silent re-extraction cannot make it
pass vacuously. Confirmed failing without the fix, passing with it.

Full suite: identical failure set before and after (42 pre-existing, Windows/env). One of
those is test_astro_import_ids.py::test_astro_relative_inputs_keep_canonical_ids, which
fails on source_file separators — the other defect in the same repro project, out of
scope here.

[graphify-labs]

Graphify reviewed this change.

Worth a look — the grounded gate found no coupling regressions or blocking issues, but 1 advisory finding(s) below merit a look before merge.

Formal verification. No changes could be formally verified in this run.

---

Graphify review — findings

This PR modifies _relativize_source_files_in in graphify/cache.py to handle CWD-relative source_file values by re-anchoring them to root-relative form when the CWD differs from the inferred root, rather than passing all relative paths through unchanged. The change targets a scenario (#2630) where relative inputs handed to extract() from a directory above the root produced cached path stamps that disagreed with how they were later read back. It also adds a new test (test_warm_hit_with_relative_inputs_from_above_the_root) exercising this case with an Astro fixture, verifying that warm cache hits reproduce cold-extraction node ids and that the .astro file is served from cache rather than re-extracted. The surface area is the single relativization helper plus its supporting test file; the many listed symbols appear to reflect module-level re-indexing rather than direct edits to each.

Worth a look

• cwd_form == root_resolved / sp comparison is always False for relative sp — graphify/cache.py:571 · Escalate · medium
  • agreed by 2 of 2 members but NOT verified (no proof, no reproducing execution) — consensus is not a verdict; needs human review

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 1177 functions depend on the 205 functions this change touches.

Health — grade A; 10 existing hotspot(s) in the area this change touches (pre-existing, not introduced here):

• extract() — 433 callers, 41 callees (high)
• _rebuild_code() — 94 callers, 51 callees (high)
• detect() — 86 callers, 13 callees (high)
• save_semantic_cache() — 50 callers, 9 callees (high)
• extract_corpus_parallel() — 26 callers, 10 callees (high)
• dispatch_command() — 2 callers, 117 callees (high)
• file_hash() — 39 callers, 6 callees (high)
• load_cached() — 39 callers, 5 callees (high)
• …and 2 more

Verification — 1177 functions in the blast radius were not formally verified this run (proofs are advisory here).

Gate & verification

graphify gate

PASS — objectively clean (no health regressions, tests not run — proofs not run this pass (advisory)). Grounded, not self-assessed.

Advisory (not blocking):

• verification_scope: 749 function(s) in the blast radius were not formally verified this run

Formal verification

Could not verify: Could not verify \_relativize\_source\_files\_in.

The verifier did not have enough to check \_relativize\_source\_files\_in, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: parameter `root` is annotated `Path` — outside the synthesizable primitive/collection set

[safishamsi]

Fixed in v0.9.41 (graphifyy==0.9.41 on PyPI). A warm cache hit no longer re-anchors a CWD-relative source_file to a ghost path when the working directory differs from the graph root; cold and warm node ids match. Thanks @rajarshidattapy.

[safishamsi]

Shipped in v0.9.41 (graphifyy==0.9.41 on PyPI). Credited in the release notes. Thanks @rajarshidattapy!