feat(doc-index): section-granularity inference, hashing, and caching fixes - #109
feat(doc-index): section-granularity inference, hashing, and caching fixes#109tkcoding wants to merge 4 commits into
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…c index Heading-based JIT retrieval needs headings that are unambiguous, evenly sized, and structurally sound, and needs to parse a document's structure once rather than on every query. toc.py gains four warning-only checks (duplicate headings, depth jumps, oversized sections, missing top-of-file description) and doc_index.py adds a cached, stat-invalidated structural index (`cfs doc-index`) with a hook for attaching per-section summaries. Fixes applied after CI and CodeRabbit review of the initial version: - The cache-validity fingerprint was path+byte_size+line_count, which can't distinguish a same-size content edit from no edit at all, and load_doc_index() read the whole file on every cache hit regardless -- defeating the "read once, not per query" point of the cache. Now uses Path.stat() (mtime_ns + size): cheaper (no read on a hit) and correctly catches same-size edits, since a write always advances mtime. - The Studio directory was resolved from the process's cwd, not the indexed file's own path -- could target the wrong project's cache. - Two silent except-and-return-None blocks (pylint's custom silent-exceptions rule) now log at debug level, following the existing decision_log.py convention. - The JIT-readiness checks were filtered through max_heading_level, whose CLI default is 3 -- hiding real issues in H4-H6 headings, exactly as seen against a real PDF-converted document during development. They now always parse every level, independent of the TOC-completeness cap. - The missing-description check accepted any frontmatter block, even one with no actual description field. - validate_toc() exceeded pylint's local-variable limit after the JIT-readiness wiring; extracted into _collect_jit_readiness_warnings. - Registered the doc-index algo and the two new toc-utils instructions in traceability-validation.md with real per-function tracing (was whole-file-scope only, tripping the granularity floor and two code-orphan-ref/code-inst-orphan validate errors). - Whitelisted annotate_section_summary in vulture_whitelist.py per this repo's existing "future caller, exercised by tests" convention. - Added tests for every fix above plus the doc_index CLI's human-output path (previously the one sub-90%-coverage file). See constructorfabric#104. Verified: full pytest suite (4800 passed; the 12 failures present with or without this change are macOS-local temp-dir path quirks and pre-existing test-order flakiness, none in the files touched here), pylint and vulture clean on the changed files, cfs validate 0 errors, spec-coverage thresholds met. Signed-off-by: TECK KEAT WILSON <yeow.teck.keat@constructor.tech>
…aleness Neither of these existed before: doc_index.py indexed every heading at every level, with no notion of "one retrievable section", and its staleness check was whole-file only -- any edit anywhere invalidated the entire cached index, making a real per-section partial rebuild impossible regardless of how small the actual edit was. infer_section_level() picks which heading level represents one real section, using the level's *frequency* as the signal: a document's real recurring structure (its chapters) shows up as the level used most often, while an occasional heading at an anomalous level -- exactly what PDF-to-Markdown conversion produces, since it assigns levels by font-size heuristics, not semantic depth -- is rare precisely because it's noise, not structure. Levels used only once are excluded as candidates outright. This is a direct, verified fix for a real failure found earlier building this feature: a real PDF-converted document put all 8 of its actual chapters on H5 and a single stray subsection on H3; treating H3 as "the" section level (or any fixed level) turned the entire back half of the document into one fake 6,601-line "section". Re-run against that same document with this change: 12 correctly-sized real sections, not one. build_doc_index() now also computes retrieval_sections -- headings grouped at exactly the inferred level (off-level stray headings stay inside whichever section they geographically fall under, rather than splitting one apart), each with a SHA-256 hash of its own text. diff_stale_sections() compares a file's current content against its last cached build at this granularity and reports which sections actually changed, matched by position (not heading text -- duplicate titles are real, see toc-heading-duplicate) -- the piece needed for a future caller to re-summarize only what changed instead of the whole document. Registered the three new instructions in traceability-validation.md; whitelisted diff_stale_sections in vulture_whitelist.py alongside annotate_section_summary (same "future caller, exercised by tests" situation). New code is 100% covered; existing sections/annotate/etag behavior is untouched and still passing. See constructorfabric#104. Verified: pytest (test_doc_index.py + test_toc.py: 156 passed; full suite: 4815 passed, the same 12 pre-existing macOS-local/flaky failures as on main, none in the files touched here), pylint and vulture clean, cfs validate 0 errors, spec-coverage thresholds met, and infer_section_level re-run against the real PDF-converted document that originally exposed the bug. Signed-off-by: TECK KEAT WILSON <yeow.teck.keat@constructor.tech>
📝 WalkthroughWalkthroughChangesDocument index and TOC readiness
Estimated code review effort: 3 (Moderate) | ~25 minutes Merge Risk: 🔵 Low · up to The change improves document sectioning and stale-section detection, but two edge cases remain: empty block descriptions may be accepted as valid, and older cached indexes may fail when reused without rebuilding. The PR is mergeable with explicit owner awareness and follow-up for these localized correctness issues. Sequence Diagram(s)sequenceDiagram
participant Operator
participant cmd_doc_index
participant get_or_build_doc_index
participant Cache
participant MarkdownFile
Operator->>cmd_doc_index: run doc-index
cmd_doc_index->>get_or_build_doc_index: request index
get_or_build_doc_index->>Cache: check metadata-matched cache
Cache->>MarkdownFile: stat file
get_or_build_doc_index->>MarkdownFile: read and parse on cache miss
get_or_build_doc_index-->>cmd_doc_index: index and cache status
cmd_doc_index-->>Operator: render JSON or human output
🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (4 passed)
Full details: Docstring CoverageExplanation Docstring coverage is 40.95% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 105 functions across 9 files. (1 skipped: 1 unsupported.)
✨ Finishing Touches🧪 Generate unit tests (beta)
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Inline comments:
In `@skills/studio/scripts/studio/commands/doc_index.py`:
- Around line 45-51: Update cmd_doc_index() to include the retrieval_sections
returned by get_or_build_doc_index() in the doc-index output, preserving their
hashes and summary slots for JSON and human-readable formats. Extend the CLI
test to cover multiple retrieval sections.
In `@skills/studio/scripts/studio/utils/doc_index.py`:
- Around line 368-376: Update annotate_section_summary() to persist the summary
on matching entries in both index["sections"] and index["retrieval_sections"]
when line_start matches, while preserving its success behavior. Add a test
verifying the retrieval_sections entry receives the annotated summary.
- Around line 179-200: Update the document-index builder around the content read
and _compute_etag call to capture file metadata before and after read_text(),
retrying the read, parsing, and index construction when the file changes during
indexing; compute the etag from the verified content state so it remains bound
to the headings and sections indexed. Add a regression test covering a
modification occurring immediately after the read and verify the resulting index
reflects a consistent file version.
- Around line 346-350: Update the section comparison logic in the function
containing old_sections and fresh_sections so unchanged and changed entries
include a unique current-section identifier, such as the current position or
line_start, alongside the heading text. Preserve positional matching and
structural_change behavior, and add a test covering duplicate headings where
each Details section remains distinguishable.
In `@skills/studio/scripts/studio/utils/toc.py`:
- Around line 841-854: The _frontmatter_has_description function currently
accepts comment-only and empty quoted description values as non-empty; update
its detection to parse the description scalar and reject blank values, YAML
comments, and empty quoted strings while continuing to recognize genuinely
populated descriptions.
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.gitignorearchitecture/features/traceability-validation.mdskills/studio/scripts/studio/cli.pyskills/studio/scripts/studio/commands/doc_index.pyskills/studio/scripts/studio/commands/validate_toc.pyskills/studio/scripts/studio/utils/doc_index.pyskills/studio/scripts/studio/utils/error_codes.pyskills/studio/scripts/studio/utils/toc.pytests/test_doc_index.pytests/test_toc.pyvulture_whitelist.py
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…abric#109 - cmd_doc_index() built its output from the index but omitted retrieval_sections/section_level in both JSON and human output -- the new data constructorfabric#109 added was invisible through the CLI. Both are exposed now, and the human formatter lists retrieval sections the same way it already lists the finer-grained ones. - A write landing between read_text() and _compute_etag() in build_doc_index() could save headings parsed from the *old* content stamped with the *new* file's etag; load_doc_index() would then treat that stale index as valid until a later edit changed the etag again. _read_with_stable_etag() brackets the read with a stat snapshot on each side and retries on mismatch, so the saved etag is provably the one that matches what was actually parsed. - diff_stale_sections() reported changed/unchanged sections by heading text alone; two sections sharing a duplicate title (a real, already-flagged possibility -- see toc-heading-duplicate) couldn't be told apart. Each entry now carries line_start alongside the heading text, which is what a caller should actually use to address "this specific section" afterwards. - annotate_section_summary() updated only index["sections"], leaving the matching retrieval_sections entry at summary=None even on success -- a caller reading retrieval_sections (the more relevant list for a future per-section summarizer) couldn't see the annotation. Now updates both when both have an entry at line_start. - toc.py's _frontmatter_has_description() accepted `description: # TODO` and `description: ""` as satisfying the check, since `#` and `"` both match \S. Now parses the field's actual value and rejects comments and empty/whitespace-only quoted strings. Extracted _compute_fresh_retrieval_sections/_position_entry out of diff_stale_sections() to stay under pylint's local-variable limit after the line_start addition; registered the new instructions (stable-read, diff-stale-helpers) in traceability-validation.md. See constructorfabric#104. Verified: pytest (test_doc_index.py + test_toc.py: 166 passed, 100% coverage on touched doc_index files); full suite: 4825 passed, the same 12 pre-existing macOS-local/flaky failures as on constructorfabric#108/constructorfabric#109, none in files touched here; pylint and vulture clean; cfs validate 0 errors; spec-coverage thresholds met; infer_section_level/retrieval_sections re-verified against the real PDF-converted document that originally exposed the granularity bug -- still 12 correct sections. Signed-off-by: TECK KEAT WILSON <yeow.teck.keat@constructor.tech>
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Inline comments:
In `@skills/studio/scripts/studio/commands/doc_index.py`:
- Around line 51-53: Update load_doc_index() to validate or migrate matching
cached indexes before cmd_doc_index() accesses section_level and
retrieval_sections; invalidate incompatible legacy entries so they are rebuilt
rather than returned unchanged. Add a regression test covering a legacy cache
without --rebuild and verify the command completes without KeyError.
In `@skills/studio/scripts/studio/utils/toc.py`:
- Line 871: Update the description validation in _check_missing_description to
reject block-scalar markers such as “|” and “>” when they have no indented
content, instead of treating the marker itself as a usable description. Detect
and validate the scalar’s actual content, preserving True only for non-empty
descriptions.
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- Push a commit to this branch (recommended)
- Create a new PR with the fixes
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architecture/features/traceability-validation.mdskills/studio/scripts/studio/commands/doc_index.pyskills/studio/scripts/studio/utils/doc_index.pyskills/studio/scripts/studio/utils/toc.pytests/test_doc_index.pytests/test_toc.py
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- architecture/features/traceability-validation.md
- tests/test_doc_index.py
- skills/studio/scripts/studio/utils/doc_index.py
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…torfabric#109 - load_doc_index() returned a cached index whenever its etag matched, with no check that the cached shape matched what this version of the code expects. A cache written before section_level/retrieval_sections existed can still have a matching etag if the file hasn't changed since -- cmd_doc_index() would then hit a KeyError reading those fields on a legacy cache instead of a clean rebuild. Now treated the same as a stale cache: rebuilt, not returned as-is. - _frontmatter_has_description() treated a YAML block-scalar marker (`description: |`, `description: >-`, ...) as a usable value, when the real content -- if any -- belongs on indented lines below it, not on the marker's own line. Now checks the first non-blank following line for real indentation before counting it as a description. See constructorfabric#104. Verified: pytest (test_doc_index.py + test_toc.py: 172 passed, 100% coverage on touched doc_index files); full suite: 4831 passed, the same 12 pre-existing macOS-local/flaky failures as before, none in files touched here; pylint and vulture clean; cfs validate 0 errors; spec-coverage thresholds met; infer_section_level/retrieval_sections re-verified against the real PDF-converted document -- still 12 correct sections. Signed-off-by: TECK KEAT WILSON <yeow.teck.keat@constructor.tech>
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tkcoding
changed the title
| "total_lines": line_count, | ||
| "sections": sections, | ||
| "section_level": section_level, | ||
| "retrieval_sections": _build_retrieval_sections(headings, lines, section_level), |
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No documented additive-only / schema-version contract for the new retrieval_sections/section_level cache fields
Severity: Minor
Problem
The PR adds retrieval_sections, section_level, and per-section hash fields to the persisted doc-index cache JSON (build_doc_index in doc_index.py). Nowhere in the codebase — not in doc_index.py's docstrings, not in architecture/features/traceability-validation.md — is there a documented contract stating that this addition is additive-only and safe for strict-schema readers, nor is there any schema-version marker a strict reader could check against.
How to reproduce
Grep doc_index.py and architecture/features/traceability-validation.md for "additive", "schema_version", "backward-compat" — none found relating to the doc-index cache format.
Expected behavior
A schema-evolution contract (e.g. a documented statement that new top-level keys are always additive, or an explicit schema_version/format_version field) so that any strict-schema consumer has a documented, checkable way to know new fields won't appear unannounced.
Actual behavior
No such contract or version marker exists anywhere in the codebase or docs. (Note: as of commit 9cf51f4, load_doc_index does now check for required-field presence to detect an old-format cache, which mitigates the practical staleness risk — but there is still no explicit version field or documented additive-only contract for future schema evolution.)
Impact
Future consumers with strict schema validation have no documented guarantee and no version field to gate on; a future breaking change to this cache format also has no version field to bump.
Suggested correction
Add a format_version (or schema_version) field to the doc-index cache dict, and document in the module docstring that new top-level keys are additive-only within a given format_version.
How to verify
After the fix, grep for the new version field in build_doc_index's returned dict and confirm docstring language stating the additive-only guarantee.
| etag_after = _compute_etag(path) | ||
| for _ in range(_MAX_READ_ATTEMPTS): | ||
| etag_before = etag_after | ||
| content = path.read_text(encoding="utf-8") |
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Non-UTF-8/binary Markdown input crashes build_doc_index with an uncaught UnicodeDecodeError
Severity: Minor
Problem
_read_with_stable_etag() in skills/studio/scripts/studio/utils/doc_index.py reads file content with path.read_text(encoding="utf-8") and no exception handling around the decode. This is the sole content-read path feeding build_doc_index(), which is in turn called by get_or_build_doc_index() and the cfs doc-index CLI command. None of these call sites check the file's content type or catch UnicodeDecodeError.
How to reproduce
from pathlib import Path
from studio.utils.doc_index import build_doc_index
p = Path("/tmp/binary.md")
p.write_bytes(b"\xff\xfe\x00\x01garbage")
build_doc_index(p) # raises UnicodeDecodeError, uncaughtEquivalently, cfs doc-index /tmp/binary.md crashes with a raw Python traceback instead of a clean CLI error.
Expected behavior
A non-Markdown or binary file passed to doc-index (or fed into build_doc_index/get_or_build_doc_index) should produce a clear, actionable error (e.g. a ui.error(...)-style message via the same error-reporting convention already used for "File not found" in cmd_doc_index), not an unhandled stack trace.
Actual behavior
path.read_text(encoding="utf-8") raises UnicodeDecodeError uncaught, propagating out of build_doc_index → get_or_build_doc_index → cmd_doc_index, producing a raw traceback and non-zero-but-uninformative failure for the CLI user.
Impact
Minor but real robustness gap: any caller pointing doc-index/build_doc_index at a binary file, a non-UTF-8-encoded text file, or an accidentally-wrong path (e.g. a PDF instead of its converted Markdown, which this feature explicitly exists to support) gets an unhandled crash instead of a diagnosable error message.
Suggested correction
Wrap the path.read_text(...) call in _read_with_stable_etag (or at the build_doc_index/cmd_doc_index boundary) in a try/except UnicodeDecodeError, and surface a clear error consistent with the existing "File not found" pattern in cmd_doc_index.
How to verify
Add a regression test that writes a file with invalid UTF-8 bytes and asserts build_doc_index/cmd_doc_index raises or reports a clear, typed error rather than an unhandled UnicodeDecodeError.
| "heading": text, | ||
| "line_start": line_start, | ||
| "line_end": line_end, | ||
| "hash": hashlib.sha256(section_text.encode("utf-8")).hexdigest(), |
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Trailing-whitespace-only edits are not staleness-inert
Severity: Minor
Problem
_build_retrieval_sections hashes section_text = "\n".join(lines[line_start-1:line_end]) verbatim via hashlib.sha256(section_text.encode("utf-8")), with no trailing-whitespace normalization. (Line-ending differences, e.g. LF vs CRLF, are already safely handled by Python's universal-newline translation in read_text() — this finding is scoped only to trailing spaces/tabs, not newline style.)
How to reproduce
- Build a doc index for a markdown file with at least two heading sections at the inferred
section_level. - Without changing any word/heading/newline, add a single trailing space to the end of one existing line inside a section, and save.
- Call
diff_stale_sections(path).
Expected behavior
A whitespace-only edit that doesn't change meaningful content should not cause diff_stale_sections to report the section as changed.
Actual behavior
The modified section's hash differs from the cached hash (trailing whitespace is part of the hashed bytes), so diff_stale_sections places it in changed, not unchanged.
Impact
Defeats the partial-rebuild/no-false-staleness optimization for a common, harmless class of edits (editor/IDE "trim trailing whitespace on save"), potentially triggering unnecessary re-summarization on every such save.
Suggested correction
Either strip trailing whitespace per line before hashing in _build_retrieval_sections (and document the normalization), or explicitly document that hashing is byte-sensitive to trailing whitespace and scope the "staleness-inert" claim to newline-sequence differences only.
How to verify
Add a regression test that builds an index, rewrites the file changing only trailing whitespace on one line within one retrieval section, and asserts the desired diff_stale_sections behavior for that case.
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| # @cpt-begin:cpt-studio-algo-traceability-validation-doc-index:p1:inst-doc-index-etag | ||
| def _compute_etag(path: Path) -> str: |
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_compute_etag can collide across genuinely different content on coarse-mtime-resolution filesystems
Severity: Minor
Problem
_compute_etag() derives the cache-validity fingerprint solely from st_mtime_ns and st_size. The docstring justifies this by claiming "a write always advances mtime," but that doesn't hold universally: on filesystems/mounts with coarse mtime resolution (some network mounts, overlay/FUSE filesystems, older FAT-family filesystems), two distinct writes to the same file within one mtime tick, each producing content of the same byte size, report an identical (mtime_ns, size) pair even though the content differs.
How to reproduce
On a filesystem with coarse mtime granularity (or by mocking Path.stat() to return the same st_mtime_ns/st_size for two different byte contents): cache an index for content A via get_or_build_doc_index(path), overwrite the file with same-length content B within the same mtime tick, then call load_doc_index(path) again — it returns the cached index built from content A.
Expected behavior
A cache-validity check should not return a hit when the file's actual content has changed, regardless of filesystem timestamp resolution.
Actual behavior
load_doc_index() compares only cached.get("etag") != current_etag; a same-size write within one mtime tick is silently treated as "unchanged" and stale cached sections/retrieval_sections are returned.
Impact
Minor but real: on affected filesystems/mounts, a caller can silently retrieve or diff against stale section content and stale summaries after a genuine edit, with no error or staleness signal. Likelihood is low on typical local disks with nanosecond mtime resolution.
Suggested correction
Either document this as an accepted, bounded limitation specific to coarse-mtime filesystems, or add an inexpensive secondary signal less prone to same-tick collisions (e.g. combining st_mtime_ns with st_ctime_ns/inode info where available).
How to verify
Add a regression test that monkeypatches Path.stat() (or the etag computation) to return identical (mtime_ns, size) for two different content strings and confirms the current stale-return behavior, then re-run after any fix.
| # @cpt-end:cpt-studio-algo-traceability-validation-doc-index:p1:inst-doc-index-build | ||
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| def _read_cache_file(cache_path: Path) -> Optional[Dict[str, Any]]: |
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All new disk-cache fallback paths in utils/doc_index.py are silent (logger.debug only), indistinguishable from a clean "no cache" state
Severity: Minor
Problem
Four new except blocks in skills/studio/scripts/studio/utils/doc_index.py handle real failure conditions (unreadable/corrupt cache file, OSError during path resolution or staleness check) but only call logger.debug(...) before falling back — no warning-level log, no field on the returned index, no signal to any caller. Sites: _index_cache_path (OSError on Studio-directory lookup), _read_cache_file (JSONDecodeError/OSError on the cache file), load_doc_index (OSError computing etag), _compute_fresh_retrieval_sections (OSError reading the file for a diff).
How to reproduce
Corrupt an existing .cache/doc-index/<slug>.json file (truncate to invalid JSON) or revoke read permission, then call get_or_build_doc_index(path) at default (non-debug) logging.
Expected behavior
A broken/corrupt/permission-denied cache should be distinguishable from a normal first-time cache miss — e.g. via a warning-level log by default, or a field on the returned index similar to cache_hit.
Actual behavior
All four paths degrade identically and silently, logged only at debug level (off by default), so a systemic problem (e.g. a permissions misconfiguration) looks exactly like normal cache misses.
Impact
Repeated, unexplained full rebuilds (defeating the "read once per file" caching this feature exists to provide) would go unnoticed without manually enabling debug logging.
Suggested correction
Promote these four to logger.warning, and/or add a boolean field such as index["cache_error"] alongside the existing cache_hit field.
How to verify
Add a regression test that corrupts a cache file and asserts a warning-level log record is emitted, or that the returned index carries an error-fallback marker.
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| # @cpt-begin:cpt-studio-algo-traceability-validation-doc-index:p1:inst-doc-index-save | ||
| def save_doc_index(path: Path, index: Dict[str, Any]) -> None: |
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save_doc_index() writes the cache file non-atomically with no cross-process lock, risking lost updates under concurrent writers
Severity: Minor-to-moderate
Problem
save_doc_index() persists the index with a plain truncating write (cache_path.write_text(json.dumps(index, indent=2), encoding="utf-8")) — no write-to-temp-then-os.replace() atomic-rename pattern, and no file lock coordinating concurrent writers. annotate_section_summary() goes through this same function after a read-modify-write cycle, which is a classic lost-update window: two processes annotating different sections of the same file's index around the same time can each load the same base index, mutate their own section, and whichever writes last silently overwrites the other's update.
How to reproduce
Two processes call annotate_section_summary(path, line_start=10, summary="A") and annotate_section_summary(path, line_start=40, summary="B") concurrently — both load the same cached index (no summaries yet), mutate their own section, and write back; whichever write_text() call lands second overwrites the other's line_start entry entirely.
Expected behavior
Either the write should be atomic (temp file + os.replace()), and/or writes should be serialized (e.g. via a lock file) so two concurrent read-modify-write cycles don't clobber each other.
Actual behavior
write_text() truncates and writes in place with no atomicity guarantee beyond a single write() syscall, and no locking — concurrent annotate_section_summary calls (or a save racing a rebuild) can race and lose updates. Note: torn reads are already safe (a partial write is caught by _read_cache_file's JSON-parse-error handling, triggering a clean rebuild) — the residual risk is specifically full read-modify-write races losing an update, not corruption.
Impact
Concurrent annotation of different sections of the same large document's index can silently drop one side's summary with no error or warning.
Suggested correction
Write to a sibling temp file and os.replace() it onto the cache path for atomicity; consider a lock file around the annotate read-modify-write cycle specifically.
How to verify
Add a regression test that runs two annotate_section_summary calls for different line_start values against the same index (simulating concurrency), and assert both summaries are present in the final saved index.
| content, | ||
| artifact_path=filepath, | ||
| max_heading_level=args.max_level, | ||
| max_section_lines=args.max_section_lines, |
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cmd_validate_toc aborts the entire multi-file validation batch on any unhandled per-file read error, discarding already-collected results
Severity: Minor-to-moderate
Problem
In skills/studio/scripts/studio/commands/validate_toc.py::cmd_validate_toc, the per-file loop only guards the "file not found" case (if not filepath.is_file()). The actual read, content = filepath.read_text(encoding="utf-8"), has no exception handling. Any other read failure on any file in the batch — permission denied, non-UTF-8/binary content, or a TOCTOU race — raises uncaught out of the loop, aborting the command before it ever reaches ui.result(...). This discards results already accumulated for every file validated earlier in the same invocation. Separately, FILE_READ_ERROR/FILE_LOAD_ERROR codes already exist in utils/error_codes.py but are unused here (error_codes isn't even imported in validate_toc.py).
How to reproduce
# files = [good.md, bad.md, good2.md]; bad.md has invalid UTF-8 bytes or revoked permissions
cmd_validate_toc([str(good), str(bad), str(good2)])
# raises uncaught after good.md was already validated and appended to `results` -- that
# result is lost, and good2.md is never reachedExpected behavior
A read failure on one file in a cfs validate-toc a.md b.md c.md batch should be recorded as a per-file ERROR result (using FILE_READ_ERROR/FILE_LOAD_ERROR), consistent with the existing "File not found" handling, and the batch should continue validating the remaining files.
Actual behavior
An unhandled exception propagates out of the loop, the command crashes with a raw traceback, and results already computed for earlier files are never emitted.
Impact
In CI or batch-validation contexts, a single bad file (encoding issue, permission glitch, or a file removed mid-run) silently destroys the whole run's output rather than surfacing that one file's problem alongside the rest.
Suggested correction
Wrap the filepath.read_text(...) call in a try/except (OSError, UnicodeDecodeError) inside the loop, append an ERROR entry to results (using error_codes.FILE_READ_ERROR/FILE_LOAD_ERROR) analogous to the existing "File not found" branch, increment total_errors, and continue to the next file.
How to verify
Add a regression test with a batch of 2+ files where one has invalid UTF-8; assert the command still emits results for the other files, marks the bad file as an ERROR with a stable error code, and does not raise.
| p = argparse.ArgumentParser( | ||
| prog="cfs doc-index", | ||
| description=( | ||
| "Build or reuse a cached heading/section index for a Markdown file, " |
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cfs doc-index --help never explains how section_level is inferred
Severity: Minor
Problem
cfs doc-index picks section_level via a frequency-based heuristic in infer_section_level(): the heading level used most often wins, levels appearing exactly once are excluded as candidates, and ties (or an all-singletons document) fall back to the shallowest level. This choice directly determines which lines get grouped into retrieval_sections in both JSON and human-readable output. None of this is mentioned anywhere a CLI user would see it.
How to reproduce
Run cfs doc-index --help (or read the argparse.ArgumentParser description in commands/doc_index.py). The description reads only: "Build or reuse a cached heading/section index for a Markdown file, so navigation reads the file's structure once, not once per query." No mention of section_level, how it's chosen, or that it can differ from the "obvious" chapter level in irregularly-leveled documents (the exact PDF-conversion scenario infer_section_level()'s own docstring cites as its motivating case).
Expected behavior
A user seeing "section_level": 5 (say) instead of the level they expected should have a way, via --help or the command's own output, to understand that the level was inferred from heading-frequency, not simply "H1/H2 is always the section level."
Actual behavior
--help gives no indication that section-level selection is heuristic at all.
Impact
Minor UX/discoverability gap — doesn't cause incorrect behavior, but makes an already-nontrivial, silently-applied heuristic harder to audit or trust from the CLI alone.
Suggested correction
Extend the argparse.ArgumentParser(description=...) in cmd_doc_index() (or add a short note to _human_doc_index()'s output) with one sentence, e.g.: "section_level is inferred from the most frequently repeated heading level (ties prefer the shallower level); a level used only once is never chosen."
How to verify
Run cfs doc-index --help after the fix and confirm the heuristic is described.
2 participants
Stacked on #108 (#108)
This branches from
jit-retrieval-doc-index(#108) —doc_index.py/toc.pydon't exist onmainyet, so until #108 merges this diff includes #108's changes too. Once #108 lands, I'll rebase this branch onto the newmain; the diff here will shrink to just what this PR adds.Summary
Infers real per-document section boundaries for JIT retrieval, hashes them for per-section staleness detection, and fixes a caching race condition, a legacy-cache crash, and two description-check gaps found during review.
Core feature
infer_section_level()picks which heading level represents one real retrievable section, using the level's frequency as the signal — PDF-to-Markdown conversion assigns heading levels by font-size heuristics, not semantic depth, so a document's real recurring structure (its chapters) shows up as the level used most often, while an occasional heading at an anomalous level is rare precisely because it's noise. Verified against the real PDF-converted document that originally exposed this bug: 12 correctly-sized sections instead of one fake 6,601-line mega-section.retrieval_sectionsgroups headings at exactly the inferred level, each with a SHA-256 hash of its own text.diff_stale_sections()compares a file's current content against its last cached build at this granularity and reports which sections actually changed, matched by position — heading text alone can't disambiguate a duplicate title.Fixes found during review (not part of the original scope)
load_doc_index()now schema-validates a cached index, not just its etag — a cache written beforesection_level/retrieval_sectionsexisted could otherwise pass a matching-etag check and then crash the caller with aKeyError._read_with_stable_etag()closes a real race: a write landing between reading a file's content and computing its etag could previously save headings from the old content stamped with the new etag, serving stale data until a later edit changed the etag again.diff_stale_sections()'s changed/unchanged entries now carryline_startalongside heading text, since two sections sharing a duplicate title otherwise can't be told apart.annotate_section_summary()now updates the matching entry in bothsectionsandretrieval_sections, not just the former.cmd_doc_index()now exposesretrieval_sections/section_levelin both JSON and human output — they existed in the index but weren't reachable through the CLI.toc.py's description check now rejects a YAML comment (description: # TODO), an empty quoted string (description: ""), and an empty block-scalar (description: |with no indented content) — previously all three satisfied the check despite carrying no real value.Test plan
pytest tests/test_doc_index.py tests/test_toc.py— 172 passed, 100% coverage on touched filespylint/vultureclean;cfs validate0 errors;spec-coveragethresholds metinfer_section_level/retrieval_sectionsre-verified against the real PDF-converted document after every fix round — still 12 correct sections