fix: skip Obsidian vault metadata directories

[rohit-jsfreaky]

Summary

This fixes vault scans where Obsidian workspace state was treated as source code.

• Add .obsidian and .smart-env to the existing unconditional generated/noise-directory set.
• Add a regression test that verifies those two Obsidian-specific directories are skipped.
• Keep generic .trash directories discoverable: the test asserts that both .trash/state.json and root project.json remain code inputs.

Why this belongs in _SKIP_DIRS

.obsidian and .smart-env contain Obsidian application metadata and plugin-generated cache data, not user-authored corpus files. A scan previously classified files such as .obsidian/graph.json and .obsidian/workspace.json as code, producing misleading graph input.

.trash is intentionally not excluded because it is a generic directory name and may contain real user files outside an Obsidian vault.

Reproduction

Create a vault root containing .obsidian/graph.json, .obsidian/workspace.json, .smart-env/state.json, .trash/state.json, and a real project.json, then call detect(root).

Before: the .obsidian JSON files appeared in files["code"].

After: .obsidian and .smart-env are excluded, while .trash/state.json and project.json remain in files["code"].

Scope

This deliberately changes only the directory-pruning list and detector coverage. It does not modify .graphifyignore behavior or user-defined exclusions.

Validation

• uv run --no-sync pytest tests/test_detect.py -q -k obsidian
• uv run --no-sync pytest tests/test_detect.py -q: 232 passed; 4 unrelated Windows baseline failures
• uv run --no-sync ruff check graphify/detect.py tests/test_detect.py
• uv run graphify update .

Fixes #2493

[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.

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Graphify review — findings

This PR adds three Obsidian-related directory names (.obsidian, .trash, .smart-env) to the _SKIP_DIRS set in graphify/detect.py, so directory traversal will exclude those paths. It also adds a new test verifying that files inside these directories are skipped while a top-level file is still detected. The large list of changed test symbols appears to reflect line-shift/reindexing from inserting the new test rather than substantive edits to those individual tests.

Worth a look

• detect() now silently omits user files under any .trash directory — graphify/detect.py:810 · 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 — 1335 functions depend on the 439 functions this change touches.

Health — this change adds coupling hotspots:

• worse: detect() — 83 callers, 13 callees

Verification — 1335 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: 708 function(s) in the blast radius were not formally verified this run

· 1 grounded finding(s) anchored inline below; 1 more finding(s) on lines outside this diff (see the check run).

[graphify-labs]

Graphify reviewed this change.

Looks safe to merge — no coupling regressions and no blocking issues, checked against the code graph (not a self-assessment).

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Graphify review — findings

This PR adds .obsidian and .smart-env to the _SKIP_DIRS set in graphify/detect.py, so Obsidian vault metadata and plugin cache directories are pruned during detection. It also adds a new test asserting these directories are skipped while an unlisted .trash directory and regular files are still included. The change targets directory-skipping behavior only.

No blocking issues surfaced. 1 lower-confidence candidate did not survive cross-model review.

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 1335 functions depend on the 439 functions this change touches.

Health — this change adds coupling hotspots:

• worse: detect() — 83 callers, 13 callees

Verification — 1335 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: 708 function(s) in the blast radius were not formally verified this run

· 1 more finding(s) on lines outside this diff (see the check run).