feat(toc,doc-index): add JIT-retrieval readiness checks and cached doc index - #108
feat(toc,doc-index): add JIT-retrieval readiness checks and cached doc index#108tkcoding wants to merge 1 commit into
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📝 WalkthroughWalkthroughAdds a cached Markdown document-index CLI command and four warning-only TOC readiness checks. The changes include cache invalidation, section summaries, configurable section limits, new warning codes, CLI wiring, and tests. ChangesDocument indexing
TOC readiness validation
Estimated code review effort: 3 (Moderate) | ~25 minutes Merge Risk: 🟡 Moderate · up to The PR adds cached document indexing and warning-only TOC readiness checks, but the cache can return stale headings and section ranges after certain edits, while absolute-path usage can select the wrong project cache and readiness warnings can be incomplete. These are bounded but concrete merge-readiness risks requiring owner follow-up before merge. Suggested reviewers: 🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (4 passed)
Full details: Docstring CoverageExplanation Docstring coverage is 33.33% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 57 functions across 8 files. (1 skipped: 1 unsupported.) ✨ Finishing Touches 💡 1🛠️ Fix failing CI checks 💡
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In `@skills/studio/scripts/studio/utils/doc_index.py`:
- Around line 34-42: The document-index cache must validate file changes using
metadata rather than the content-insensitive _compute_etag formula or read_text
on every hit. Update load_doc_index and its cache metadata to store st_mtime_ns
and st_size, call Path.stat() before loading a cached index, and reuse the cache
only when both values match; add a regression test replacing a heading with
same-size, same-line-count text to verify stale headings and section ranges are
not returned.
- Line 54: Update the Studio directory lookup in the doc-index flow to call
find_studio_directory with path.resolve().parent instead of Path.cwd(), ensuring
the cache is resolved from the indexed file’s project directory.
In `@skills/studio/scripts/studio/utils/toc.py`:
- Around line 856-859: Update the frontmatter handling in the description-check
flow around _find_frontmatter_end so it suppresses the warning only when the top
YAML block contains a non-empty accepted description field. Do not return early
for frontmatter containing only unrelated fields such as title; preserve the
existing line-count and warning behavior otherwise.
- Around line 987-990: Update the readiness checks around
parse_headings_with_lines and _check_duplicate_heading_titles,
_check_heading_depth_jumps, and _check_section_lengths to parse all heading
levels without applying max_heading_level. Retain max_heading_level exclusively
for TOC validation, and ensure ignored headings are included when determining
section boundaries for length validation.
🪄 Autofix
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
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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>
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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>
…ctorfabric#110 Adding commands/tfidf.py and commands/okf.py (both whole-file-scope claims, no instruction tracing) dropped the repo's spec-coverage granularity below its floor (0.4593 < 0.4600) -- the exact same failure shape constructorfabric#108 hit for utils/doc_index.py originally. commands/doc_index.py had the same gap already (pre-existing, just under the floor's margin until now). Added real @cpt-begin/@cpt-end instruction markers to all three command wrappers' main function and human-output formatter, registered as Supporting instructions under each module's existing algo ID. Along the way, instrumenting all three surfaced a real pylint duplicate- code finding: all three commands independently reimplemented the same "resolve a file-path CLI argument, emit the standard File-not-found ERROR result, return exit code 2" block. Extracted into ui.require_existing_file(), shared by all three (and available to any future single-file-argument command), registered under core-infra.md's existing render-info-human algo alongside ui.py's other generic helpers. See constructorfabric#104. Verified: pytest (test_tfidf.py + test_okf.py + test_doc_index.py + test_toc.py + test_ui_human_mode.py: 346 passed, 100% coverage on the three command files, 97% on ui.py full-suite); full suite: 4869 passed, the same 12 pre-existing macOS-local/flaky failures seen throughout this feature's development, none in files touched here; pylint and vulture clean (duplicate-code finding resolved, not suppressed); cfs validate 0 errors; spec-coverage thresholds met; TF-IDF re-verified against the real PDF-converted document after the refactor -- still reproduces the documented "zero-shot" margin (1.06x) exactly. Signed-off-by: TECK KEAT WILSON <yeow.teck.keat@constructor.tech>
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Automated Deep Review — 5 Major findings out of 66 checks run across 7 thematic phases (each independently adversarially verified). Full plan and 12 additional Minor findings available on request.
| content, | ||
| artifact_path=filepath, | ||
| max_heading_level=args.max_level, | ||
| max_section_lines=args.max_section_lines, |
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JIT-readiness warnings invisible in human CLI output
Severity: Major
Problem
The human-readable output branch for a WARN-only file (_human_validate_toc's final else:, line 134) prints only f"{path}: {status}" and never iterates r.get("warnings", []), unlike the FAIL branch just above it which does. Since this PR's four new JIT-retrieval readiness checks (duplicate headings, heading-depth jumps, oversized sections, missing description) are warning-only by design, any file that trips only these new checks lands in this silent branch. (Anchored here at the new max_section_lines wiring since line 134 itself isn't touched by this diff, but its behavior is what this PR's new warnings now depend on.) Separately, _human_doc_index in commands/doc_index.py never prints the target file name either.
How to reproduce
- Create a Markdown file with one duplicate heading title and no other TOC issues.
- Run
cfs validate-toc file.md(human mode, no--json).
Expected behavior
The new warning (e.g. toc-heading-duplicate: ...) is printed, the same way an error would be under FAIL.
Actual behavior
Output is just file.md: WARN with no indication of what's wrong — the JSON output (--json) does contain the warning, so the information exists but never reaches the default human-facing path.
cmd_validate_toc()
-> validate_toc() returns {status: "WARN", warnings: [...]}
-> _human_validate_toc()
status == "WARN" --> else: branch
prints "path: WARN" only
(warnings list never read)
Impact
The PR's headline feature (JIT-readiness warnings) is effectively invisible to anyone using the default CLI output instead of --json.
Suggested correction
Add a branch for status == "WARN" (or extend the else) that iterates r.get("warnings", []) the same way the FAIL branch iterates r.get("errors", []); print data["file"] in _human_doc_index.
How to verify
Add/extend a TestCmdValidateToc case: a file with exactly one warning and no errors, run through cmd_validate_toc's human-output path, and assert the warning text appears in the captured output.
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| if cached.get("etag") != current_etag: | ||
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| return cached |
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Cache read has no shape/key validation, causing unhandled KeyError
Severity: Major
Problem
load_doc_index validates only the etag key before returning the cached dict as-is. It never checks that the other required keys (total_lines, sections, etc.) are present. Downstream code (commands/doc_index.py, annotate_section_summary) indexes into the result with bare [...], not .get(...).
How to reproduce
- Run
cfs doc-index file.mdonce to create the cache file under.cache/doc-index/<slug>.json. - Hand-edit that JSON to remove the
"sections"key, leaving"etag"untouched (source file unmodified, so the etag still matches). - Run
cfs doc-index file.mdagain without--rebuild.
Expected behavior
A malformed/incomplete cache should be treated like a stale or corrupt one — logged and rebuilt (the module's own docstring says load_doc_index returns None "if missing/stale/absent").
Actual behavior
load_doc_index returns the truncated dict as a valid hit, and commands/doc_index.py's len(index["sections"]) raises an unhandled KeyError: 'sections'.
load_doc_index(path)
etag matches -> return cached (no key-shape check)
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cmd_doc_index(): index["sections"] --> KeyError: 'sections'
Impact
A partially-written or hand-edited cache file crashes the CLI with a raw traceback instead of a documented error or automatic rebuild.
Suggested correction
After the etag check in load_doc_index, validate the presence of required keys ({"etag", "total_lines", "sections"} at minimum); treat a mismatch the same as stale/corrupt (log and return None).
How to verify
Add a test that writes a cache file with a matching etag but a missing required key, then asserts load_doc_index returns None (and/or that cmd_doc_index transparently rebuilds rather than raising).
| any real edit (including a same-size, same-line-count text swap, since | ||
| a write always advances mtime), so it still catches content changes; a | ||
| byte-count/line-count-only fingerprint would not (two edits that happen | ||
| to preserve both would silently look unchanged, and computing either |
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mtime+size cache etag can silently miss same-size edits
Severity: Major
Problem
The cache-validity fingerprint is f"{st.st_mtime_ns}:{st.st_size}" — filesystem metadata only, no content hash. The docstring above it asserts this is safe unconditionally ("a write always advances mtime"), but that isn't universally true: filesystems with coarse mtime resolution (FAT32, classic HFS+, many NFS mounts) can give two same-size edits within one mtime tick an identical etag.
How to reproduce
On a filesystem with ≥1s mtime granularity:
- Write a file with heading "Section A"; call
get_or_build_doc_index(caches etagT:N). - Within the same mtime tick, overwrite with same-length content renaming the heading to "Section Z".
- Call
get_or_build_doc_indexagain.
Expected behavior
The cache should detect the content change and rebuild.
Actual behavior
_compute_etag returns the same T:N string, so the stale cache (still showing "Section A") is returned as a valid hit. Notably, this PR's own regression test (test_same_size_same_line_count_edit_is_still_detected_as_stale) has to manually call os.utime(f, ns=(..., st.st_mtime_ns + 1)) to force the mtime forward — direct evidence that the "always advances mtime" assumption doesn't hold reliably even in this PR's own test environment.
write("...Section A...") -> etag = T:N -> cache saved
write("...Section Z...") (same size, same mtime tick)
-> etag = T:N (unchanged!)
-> load_doc_index(): cached.etag == current_etag -> HIT (stale data returned)
Impact
Silent false cache hit — stale headings/sections/summaries served with no error surfaced anywhere.
Suggested correction
Either document this as an explicit, accepted limitation (call out filesystem mtime granularity in the docstring), or add a stronger invalidation signal (e.g. a monotonic write-generation counter, or falling back to a content hash when size matches but the edit is suspiciously fast).
How to verify
On a filesystem/test harness that can simulate coarse mtime resolution (or by monkeypatching Path.stat() to return identical st_mtime_ns/st_size across two different contents), confirm the cache is invalidated regardless.
| MIN_LINES_FOR_DESCRIPTION_CHECK = 100 | ||
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| def _check_duplicate_heading_titles( |
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Duplicate-heading check misses case/whitespace variants and doesn't skip front-matter
Severity: Major
Problem
_check_duplicate_heading_titles compares raw heading text via a plain dict with no case-folding or whitespace normalization, and the heading list it operates on (parse_headings_with_lines) has no YAML front-matter skip (unlike _check_missing_description, which does skip front-matter). No unicodedata.normalize call exists anywhere in the file either, so NFC/NFD-distinct but visually-identical headings are also missed by the same root cause.
How to reproduce
Parse a document containing:
---
title: Foo
# this is a note
---
## Section
## section
## Setup Guide
## Setup GuideExpected behavior
"Section"/"section" and "Setup Guide"/"Setup Guide" (double space) should be flagged as duplicates; the # this is a note line inside front-matter should not be parsed as a real heading.
Actual behavior
None of the four headings above are flagged as duplicates, and the front-matter comment line is parsed into the heading list, potentially throwing off depth-jump and section-length checks that consume the same list.
parse_headings_with_lines(lines)
no front-matter awareness --> "# this is a note" counted as H1
_check_duplicate_heading_titles(headings)
seen[text] keyed on raw text --> "Section" != "section" (case)
--> "Setup Guide" != "Setup Guide" (whitespace)
Impact
Silently defeats the duplicate-heading check (and pollutes the shared heading list used by the other three JIT-readiness checks) for a common class of real-world documents.
Suggested correction
Normalize heading text (casefold + collapse internal whitespace + NFC-normalize) before using it as the seen dict key, while still reporting the original text in the warning payload; skip front-matter lines in parse_headings_with_lines (reuse the existing _find_frontmatter_end helper).
How to verify
Add test cases for case-only duplicates, whitespace-only duplicates, NFC/NFD-only duplicates, and a front-matter block containing a #-prefixed line, asserting the expected warnings/non-warnings.
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| Thin CLI wrapper around ``studio.utils.doc_index``. | ||
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| @cpt-flow:cpt-studio-flow-traceability-validation-validate:p1 |
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CPT @cpt-flow tag references the wrong, unrelated flow
Severity: Major
Problem
This module docstring adds @cpt-flow:cpt-studio-flow-traceability-validation-validate:p1. That ID is the pre-existing "Validate Artifacts" flow (cfs validate), already correctly tagged as a bare #-comment directly above cmd_validate in commands/validate.py:1230. None of that flow's steps (load context, resolve artifacts, cross-validate, etc.) relate to doc-index in any way.
How to reproduce
Run cfs where-used --id cpt-studio-flow-traceability-validation-validate after this PR merges.
Expected behavior
Only commands/validate.py's cmd_validate should be attributed to this flow ID; cfs doc-index should either have no @cpt-flow tag, or a real one describing its own flow.
Actual behavior
doc_index.py is now also attributed to the Validate-Artifacts flow, polluting cfs where-used/cfs validate traceability/coverage data for that flow, while the real cfs doc-index feature ends up with zero flow-level traceability of its own. The tag is also placed inside the module docstring rather than as a bare comment directly above the entry-point function, unlike every other @cpt-flow usage in this codebase.
cpt-studio-flow-traceability-validation-validate
correctly tagged: commands/validate.py:1230 (above cmd_validate)
ALSO tagged: commands/doc_index.py:7 (unrelated command, docstring)
-> traceability tooling now double-counts this flow ID
Impact
Corrupts the traceability data this feature exists to protect — the exact opposite of what a traceability-validation PR should do.
Suggested correction
Remove the stray @cpt-flow tag from doc_index.py's docstring. If a flow-level definition is actually wanted for cfs doc-index, add a real cpt-studio-flow-... entry to architecture/features/traceability-validation.md and reference that ID as a bare #-comment directly above def cmd_doc_index.
How to verify
Run cfs where-used --id cpt-studio-flow-traceability-validation-validate (or the equivalent traceability query) and confirm it reports only commands/validate.py.
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Automated Deep Review — 12 Minor findings (10 inline below). Two more without a diff-anchorable line:
- No Unicode (NFC/NFD) normalization in duplicate-heading comparison (same root cause and same fix as the Major finding on
_check_duplicate_heading_titlesin the prior review — addunicodedata.normalize("NFC", text)alongside the casefold/whitespace fix). skills/studio/studio.clispecnot updated for the newdoc-indexcommand or thevalidate-toc --max-section-linesflag. This file isn't touched by this PR's diff at all, so it can't be anchored inline. It's the repo's maintained per-command CLI reference (COMMAND/SYNOPSIS/OPTIONS/EXIT CODES/OUTPUT blocks for all 38 dispatchable commands) — noCOMMAND doc-indexentry exists, andvalidate-toc's OPTIONS block doesn't list the new flag. Doc-only gap, no evidence of CI enforcement, so kept Minor.
| 6. [x] - `p1` - Validate TOC: check existence, anchor validity, completeness, staleness - `inst-toc-util-validate` | ||
| 7. [x] - `p1` - Parse headings with line numbers, fence-aware (shared by doc-index and the JIT-retrieval readiness checks, which need section boundaries the plain heading list doesn't carry) - `inst-toc-util-parse-headings-lines` | ||
| 8. [x] - `p1` - Collect JIT-retrieval readiness warnings for a document: gathers all four signals below over *every* heading level, independent of whatever level cap the caller configured for TOC-completeness checking - `inst-toc-jit-readiness-collect` | ||
| 9. [x] - `p1` - Compute the four JIT-retrieval readiness signals -- duplicate heading titles, heading depth jumps, oversized sections (`--max-section-lines`), and a missing top-of-file description/frontmatter block -- all warning-only, never errors (see constructorfabric/studio#104) - `inst-toc-jit-readiness` |
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Spec doc field-shape mismatch and missing defaults/output fields
Severity: Minor
Problem
This spec doc describes --max-section-lines by name here but never states its default (300, DEFAULT_MAX_SECTION_LINES in utils/toc.py). The pre-existing "Validate TOC" return-shape line a few lines up (**RETURN** JSON: {status, files_checked, errors}, line 402) doesn't match the actual output shape ({status, files_validated, error_count, warning_count, results}) even before this PR — and this PR's new warning codes (toc-heading-duplicate, toc-heading-depth-jump, toc-section-too-long, toc-missing-description) aren't named anywhere either. Separately, the "Document Index" section below never enumerates cfs doc-index's exact JSON output fields.
How to reproduce
Read the "Validate TOC" section expecting to find the four new warning-code strings or the --max-section-lines default; read the "Document Index" section expecting the cfs doc-index output field list.
Expected behavior
The doc should state the default value and the exact field/error-code names as the authoritative contract.
Actual behavior
Neither is present — the default and the literal codes/field names must be discovered by reading source/tests instead of the spec.
traceability-validation.md line 402: RETURN JSON: {status, files_checked, errors} <- stale, wrong field names
actual: {status, files_validated, error_count, warning_count, results}
line 422: mentions --max-section-lines by name, no default value stated
Document Index section: no output-field enumeration for `cfs doc-index`
Impact
Spec doc is misleading/incomplete as a contract reference for both commands touched by this PR.
Suggested correction
Update the stale return-shape line at 402 to the actual field names, add the --max-section-lines default here, and add an output-fields line to the Document Index section.
How to verify
Cross-read the updated doc against commands/validate_toc.py's and commands/doc_index.py's actual output dicts and confirm every field/code name matches.
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| def _check_section_lengths( |
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--max-section-lines unguarded against nan/negative at the gate-function layer
Severity: Minor
Problem
_check_section_lengths/validate_toc's max_section_lines parameter has no independent validation inside this function — only the CLI's argparse(type=int) layer blocks non-numeric junk.
How to reproduce
Call validate_toc(content, max_section_lines=float('nan')) or validate_toc(content, max_section_lines=-1) directly as a library call, bypassing the CLI.
Expected behavior
A non-numeric/out-of-range value should be rejected or explicitly classified by the function itself, independent of any CLI wrapper.
Actual behavior
float('nan') silently disables the oversized-section check entirely (x > nan is always False), and a negative value flags virtually every section — no explicit error in either case.
validate_toc(content, max_section_lines=float('nan')) # oversized-section warnings never fire
validate_toc(content, max_section_lines=-1) # every section flagged
Impact
A caller using the Python API directly (not the CLI) gets silently wrong behavior instead of a clear error.
Suggested correction
Clamp/validate max_section_lines inside validate_toc/_check_section_lengths itself, independent of the CLI's argparse type guard.
How to verify
Add unit tests calling validate_toc/_check_section_lengths directly with nan, inf, and a negative value, asserting either a raised error or documented classification.
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No schema-version marker on the doc-index cache
Severity: Minor
Problem
The index dict returned here has no schema_version/version field, and load_doc_index only compares etag, never a version marker.
How to reproduce
Ship a future Studio version that changes the sections shape; run against a project with an existing cache built by the old version and an unchanged source file (etag still matches).
Expected behavior
A future schema change should be detectable and trigger an explicit rebuild/error rather than silently returning old-shape data.
Actual behavior
This is a brand-new, local-only, gitignored cache with no existing incompatible format to worry about yet, so today there is no active bug — but nothing would catch a future mismatch either.
build_doc_index() -> {"path","etag","built_at","total_lines","sections"} # no schema_version
load_doc_index() -> only checks cached.get("etag") != current_etag
Impact
Forward-looking hardening gap, not an active bug today.
Suggested correction
Add a SCHEMA_VERSION constant, embed it here, and check it alongside etag in load_doc_index.
How to verify
Bump the constant in a follow-up schema change and confirm old caches are rejected/rebuilt rather than returned as-is.
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| # @cpt-begin:cpt-studio-algo-traceability-validation-doc-index:p1:inst-doc-index-annotate | ||
| def annotate_section_summary(path: Path, line_start: int, summary: str) -> bool: |
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annotate_section_summary is unreachable from any production code path
Severity: Minor
Problem
annotate_section_summary is not called from any production code path in this PR — only from tests, and imported into vulture_whitelist.py purely to silence the unused-symbol linter.
How to reproduce
Search the repo for callers of annotate_section_summary outside tests/test_doc_index.py and vulture_whitelist.py.
Expected behavior
A shipped, non-test-only function should have at least one reachable production caller, or be clearly marked as forward-looking API.
Actual behavior
Zero production callers exist; it's genuinely speculative code for a documented "future LLM caller" per its own docstring — transparent and tested, not hidden, but unreachable outside tests today.
annotate_section_summary()
callers: tests/test_doc_index.py (6 sites), vulture_whitelist.py (import only)
callers in commands/doc_index.py or cli.py: none
Impact
No runtime risk; purely a maintainability/clarity note.
Suggested correction
No change required for merge; consider tracking a follow-up issue for when the LLM-caller integration actually lands, since right now there's no way to reach this function from cfs doc-index.
How to verify
N/A — informational; nothing to verify until a real caller is wired in.
| # @cpt-end:cpt-studio-algo-traceability-validation-toc-utils:p1:inst-toc-util-parse-headings | ||
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| # @cpt-begin:cpt-studio-algo-traceability-validation-toc-utils:p1:inst-toc-util-parse-headings-lines | ||
| def parse_headings_with_lines( |
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Heading-parsing logic duplicated between parse_headings and parse_headings_with_lines
Severity: Minor
Problem
This function duplicates the fence-tracking/heading-matching loop of the pre-existing parse_headings almost line-for-line, rather than having one delegate to the other (the docstring explains this was a deliberate choice to avoid touching parse_headings's existing 2-tuple call sites).
How to reproduce
Compare parse_headings (existing) and parse_headings_with_lines (new) side by side — both independently call _fence_update and _HEADING_RE in the same sequence.
Expected behavior
A future fix to fence-detection or the heading regex should apply to both functions automatically.
Actual behavior
A future fix applied to only one of the two would silently diverge them, since there is no shared implementation.
parse_headings() parse_headings_with_lines()
loop: _fence_update() loop: _fence_update() <- duplicated
_HEADING_RE.match() _HEADING_RE.match() <- duplicated
Impact
Maintenance/drift risk, not an active bug.
Suggested correction
Have parse_headings delegate to parse_headings_with_lines internally and strip the line numbers, or extract the shared fence/heading-match loop into one private generator both functions consume.
How to verify
After refactoring, confirm both functions' existing test suites still pass unchanged (behavior-preserving refactor).
| # @cpt-end:cpt-studio-algo-traceability-validation-toc-utils:p1:inst-toc-jit-readiness-collect | ||
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| # @cpt-begin:cpt-studio-algo-traceability-validation-toc-utils:p1:inst-toc-util-validate | ||
| def validate_toc( |
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No opt-out for the four new warning-only checks
Severity: Minor
Problem
The four new JIT-readiness checks run unconditionally inside validate_toc() — there's no flag to disable them as a group (only --max-section-lines tunes one threshold).
How to reproduce
Run cfs validate-toc on a large legacy doc corpus with many long-standing oversized sections or duplicate headings.
Expected behavior
A team should be able to quiet noisy warnings for files/repos where they aren't actionable, without weakening the check globally.
Actual behavior
Every run emits WARN for these files with no way to suppress all four short of raising --max-section-lines globally (which weakens that one check for everyone, and does nothing for the other three checks).
validate_toc(content)
_collect_jit_readiness_warnings() always runs, no disable flag
only knob: --max-section-lines (threshold, not on/off)
Impact
Low severity since the checks are warning-only and never affect exit code — a real but non-blocking UX gap.
Suggested correction
Optional — consider a --skip-readiness-checks flag if teams later report warning fatigue; not blocking for this PR.
How to verify
N/A unless implemented — then verify the flag suppresses all four warning codes.
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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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Cache write is not atomic
Severity: Minor
Problem
save_doc_index writes the cache file directly (cache_path.write_text(...)) rather than atomically (temp file + os.replace). Two concurrent processes building/saving the same file's cache could interleave writes.
How to reproduce
Run two processes concurrently calling get_or_build_doc_index for the same file with force_rebuild=True, racing on the same cache path.
Expected behavior
A reader should never observe a torn/partial write, ideally via an atomic rename.
Actual behavior
A reader mid-write could see truncated/invalid JSON. This matches the rest of the codebase's existing convention (not unique to this PR), and load_doc_index's existing except (json.JSONDecodeError, OSError): return None — backed by a dedicated passing test — already turns a torn/corrupt read into a safe, self-healing rebuild rather than propagated corruption, so the practical risk is low.
Process A: write_text(partial...) ─┐
Process B: read_text() ------------┘--> JSONDecodeError -> load_doc_index returns None -> safe rebuild
Impact
Low — bounded by the existing corrupt-cache fallback; worst case is a wasted rebuild, not silent corruption reaching a caller.
Suggested correction
Optional hardening — write to a temp file and os.replace() into place.
How to verify
A concurrency stress test writing/reading the same cache path from multiple processes/threads, asserting no unhandled exception ever surfaces to the caller.
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| def _check_missing_description( |
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Missing-description check is front-matter-only, flags badge/blurb READMEs
Severity: Minor
Problem
_check_missing_description only recognizes a description declared inside a YAML front-matter description: field.
How to reproduce
Create a >100-line document with a title, badge images, and a genuine one-line prose blurb directly under the title, but no YAML front-matter block, followed by a normal ## Table of Contents.
Expected behavior
A document with a clear, human-readable description near the top should not be flagged as missing one, regardless of whether it uses YAML front-matter.
Actual behavior
The document is still flagged toc-missing-description — a plausible false positive for common README styles. (A nearby test's docstring references "CodeRabbit PR #108," suggesting this front-matter-only scope was already discussed and may be intentional design rather than an oversight.)
Doc: # Title\n[badge][badge]\nThis tool does X for people who need Y.\n## Table of Contents
_check_missing_description(): no YAML front-matter found -> toc-missing-description (even though a real blurb exists)
Impact
Possible noisy false positives on README-style docs that don't use YAML front-matter.
Suggested correction
Optional — rename the check/message to explicitly say "no YAML front-matter description field" so it reads as scoped rather than "no description at all"; or extend detection to accept a short prose blurb before the first ## heading.
How to verify
Add a test with a badge+blurb, no-front-matter document and assert the intended (documented) behavior, whichever is chosen.
| codes = [w["code"] for w in result["warnings"]] | ||
| assert "toc-missing-description" in codes | ||
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| def test_jit_readiness_warnings_are_never_errors(self): |
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Test coverage gap: warning-only guarantee not proven via full CLI path
Severity: Minor
Problem
This is the only test exercising all four new warning codes together, but it also deliberately trips an unrelated pre-existing TOC-completeness error, and it calls validate_toc() directly rather than cmd_validate_toc.
How to reproduce
Read test_jit_readiness_warnings_are_never_errors and check whether it asserts an exit code via the CLI entry point.
Expected behavior
A dedicated test should prove "all four warnings, zero errors -> cmd_validate_toc returns 0" end-to-end.
Actual behavior
No such test exists — the behavior looks correct by code inspection (cmd_validate_toc returns 2 only if total_errors), but it's unverified end-to-end for the all-four-warnings, zero-errors case.
test_jit_readiness_warnings_are_never_errors()
calls validate_toc() directly, also trips an unrelated error
-> does not prove: cmd_validate_toc([...]) == 0 when ONLY warnings fire
Impact
A regression in cmd_validate_toc's exit-code logic for the warn-only case would not be caught by the current suite.
Suggested correction
Add a TestCmdValidateToc case with a document tripping all four JIT codes and a clean/complete TOC (no completeness/staleness errors), asserting rc == 0 and status == "WARN" with warning_count >= 4.
How to verify
Run the new test and confirm it fails if cmd_validate_toc's exit-code branch is deliberately broken (mutation check).
| f = _write(tmp_path) | ||
| rc = cmd_doc_index([str(f)]) | ||
| assert rc == 0 | ||
| out = json.loads(capsys.readouterr().out) |
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Test coverage gap: corrupted-cache auto-rebuild not proven at CLI/exit-code level
Severity: Minor
Problem
This test only asserts load_doc_index(f) is None for a corrupted cache file — it never calls cmd_doc_index([...]) afterward to confirm the command-level exit code stays 0 when transparently rebuilding after corruption.
How to reproduce
Read test_load_returns_none_on_corrupt_cache_file and check whether it calls cmd_doc_index after corrupting the cache.
Expected behavior
A dedicated test should prove the full CLI path recovers cleanly (rc == 0, fresh rebuild) from a corrupted on-disk cache.
Actual behavior
No such end-to-end test exists — the underlying behavior looks safe by inspection (the except (json.JSONDecodeError, OSError) path returns None, triggering a rebuild), but it's unverified at the CLI/exit-code layer.
test_load_returns_none_on_corrupt_cache_file()
asserts load_doc_index(f) is None only
-> does not call cmd_doc_index([str(f)]) to confirm rc == 0
Impact
A regression in the CLI's handling of the rebuild-after-corruption path would not be caught by the current suite.
Suggested correction
Add a test that corrupts the cache file the same way, then calls cmd_doc_index([str(f)]) and asserts rc == 0 and cache_hit is False.
How to verify
Run the new test and confirm it fails if the corrupt-cache fallback path is deliberately broken (mutation check).
No Unicode (NFC/NFD) normalization in duplicate-heading comparisonSeverity: Minor Problem How to reproduce Expected behavior Actual behavior Impact Suggested correction How to verify
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Summary
toc.pygains four warning-only JIT-retrieval readiness signals: duplicate heading titles, heading depth jumps, oversized sections (configurable--max-section-lines, default 300), and a missing top-of-file description — structural properties that make heading-based JIT retrieval harder without invalidating otherwise-valid documents.doc_index.py(util +cfs doc-indexcommand): a cached, etag-invalidated structural index (headings + section line ranges) so navigation reads a file's structure once per file, not once per query, with anannotate_section_summaryhook for a future LLM caller to attach per-section summaries.See #104.
Test plan
pytest tests/test_toc.py tests/test_doc_index.py— 132 passeddoc-index/evalboth resolve correctly via the CLI dispatch table after rebasing onto currentmainSummary by CodeRabbit
New Features
doc-indexcommand to build, reuse, inspect, and rebuild structural indexes for Markdown documents.Validation Improvements