Index a local folder containing documentation files (.md, .txt, .rst; plus .pdf/.docx/.pptx/.epub when the optional [office] extra is installed — converted to Markdown locally). Parses by heading hierarchy into sections for efficient retrieval. An already-indexed source is recognized before storage is chosen: the established handle is reused (or refreshed), an explicit conflicting name returns a conflict instead of creating a duplicate index, and multiple equivalent legacy indexes return bounded ambiguity. Embeddings auto-enable when a provider is configured (GOOGLE_API_KEY, OPENAI_API_KEY, openai-compatible + JDOCMUNCH_OPENAI_COMPAT_URL + JDOCMUNCH_OPENAI_COMPAT_MODEL, or sentence-transformers).

Index a GitHub repository's documentation. Fetches .md/.txt files, parses sections, and saves to local storage. Embeddings auto-enable when a provider is configured (GOOGLE_API_KEY, OPENAI_API_KEY, openai-compatible + JDOCMUNCH_OPENAI_COMPAT_URL + JDOCMUNCH_OPENAI_COMPAT_MODEL, or sentence-transformers).

List all indexed documentation repositories.

v1.56+ — single-call repo snapshot: doc_count, section_count, total_byte_size, format_breakdown, top_tags, top_roles, indexed_at. Composition of v1.46/v1.50/v1.55 aggregations. Use for 'what is this repo at a glance?'

v1.58+ — single-doc detail view. Pairs with list_docs (cross-doc inventory). Returns section list (handles), role_distribution, tag_distribution, byte_size, format, indexed_at for one doc. No content reads.

v1.55+ — flat per-doc inventory of an indexed repo: doc_path, section_count, format, byte_size for each indexed document. Lighter than get_toc_tree (which returns full section trees per doc). Sorted by doc_path.

Get a flat table of contents for all sections in a repo, sorted by document order. Content is excluded — use get_section to retrieve content.

Get a nested table of contents tree per document. Shows parent/child heading relationships. Content is excluded.

Get the section hierarchy for a single document file, without content.

Search sections by relevance. Hybrid (BM25 lexical + semantic embedding) fusion when the index was built with use_embeddings=true; falls back to lexical-only otherwise. Returns summaries only — use get_section for full content.

v1.59+ — count sections matching the same filter set as search_sections (path_glob, role/roles/exclude_roles, tags/exclude_tags, min/max_level, min/max_byte_length) but skip ranking. Use for UI counters or 'does anything match?' probes.

v1.57+ — fast title-only token-overlap match. Different from search_sections (full hybrid retrieval). Use for navigation: 'find the section whose heading text matches X'. Handle-only output ({id, title, level, doc_path, _score}); no content reads, no embeddings.

Retrieve the full content of a specific section using byte-range reads. Use after identifying section IDs via search_sections or get_toc.

Batch content retrieval for multiple sections in one call.

Retrieve a section with its full hierarchy context: ancestor headings (root → parent) for orientation, the target section's content, and immediate child summaries. Prevents 'section too thin' without falling back to whole-file reads.

v1.54+ — consolidated handle bundle: full metadata + ancestor breadcrumb + prev/next/parent/first_child neighbors for one section in a single call. Saves three round-trips vs calling get_section_summary + get_section_path + section_neighbors separately. No content reads.

v1.37+ — return prev/next siblings (in document order), parent, and first child for a section. Handles only (id, title, level, doc_path) — no content. Use for fast sequential navigation without re-querying search_sections.

v1.47+ — list sections that have drifted from index state (edited_uncommitted or stale_index buckets via the v1.16 FreshnessProbe). By default compares the index against the cached raw-content mirror, NOT live workspace files; pass live_source=true to read the live files under the index's source_root. _meta.drift_layer reports which layer ran. Pre-flight check before deciding whether to re-index. Handle-only — no content reads.

v1.50+ — list every distinct role classification across the repo with per-role section counts and id samples. Companion to v1.46 get_all_tags. Sections without metadata.role are bucketed under 'unknown'. Use to discover what roles exist before constructing a role= or profile= query.

v1.46+ — list every unique #hashtag across the repo with per-tag section counts. Companion to the v1.45 tags filter on search_sections — use this to discover what tag namespaces exist before constructing a tag-filtered query. Lowercase-normalized.

v1.43+ — return every descendant of a section (BFS over parent_id) in document order with depth offset. Pairs with get_section_path (ancestors). Optional max_depth caps the walk; max_depth=1 returns immediate children only. Handles only — no content.

v1.49+ — batch counterpart to get_section_excerpt. Resolves N previews in one call against a single index load. Per-id errors reported in-line. _meta.tokens_saved aggregates byte savings across the batch.

v1.41+ — return a short content preview (default 500 bytes) for one section. Trimmed to last newline before the cap so it ends on a paragraph boundary. Use to peek at content before paying for a full get_section read. _meta.tokens_saved reports the byte-savings vs full content.

v1.40+ — return the breadcrumb chain (root → ... → target) for a section_id. Walks parent_id upward; cycle-protected. Handles only ({id, title, level, doc_path}) per step plus depth.

v1.39+ — list sections whose doc_path receives zero inbound references from any other doc. Companion to get_broken_links and get_stale_pages: documentation that exists but nobody links to.

v1.38+ — return full indexed metadata (title, summary, role, tags, metadata, parent_id, children, content_hash, byte_start/end, byte_length) for one section without fetching content. Use to inspect role/tags before deciding whether to read the content via get_section.

v1.48+ — batch version of get_section_summary. Resolve metadata for many ids in one call against a single index load. Per-id errors are reported in-line on the corresponding result entry rather than aborting the batch.

Remove a repo index and its cached raw files.

Scan indexed doc files for internal cross-references that no longer resolve. Checks markdown links, RST :ref:/:doc: directives, and anchor-only links (#heading). External links (http/https) are skipped. Output: list of {source_file, source_section, target, reason} where reason is 'file_not_found', 'section_not_found', or 'anchor_not_found'.

Check which jcodemunch symbols have matching documentation in this doc index. Given a list of jcodemunch symbol IDs, reports which symbols are mentioned in section titles (documented) vs absent (undocumented). Bridges jcodemunch <-> jdocmunch. symbol_ids capped at 200. Output: {documented, undocumented, coverage_pct}.

Find all sections that link TO a given document (inverse reference graph). Useful for the LLM Wiki pattern: when a source changes, find which wiki pages reference it. Output: list of {source_file, source_section, source_section_id, link}.

Find wiki pages whose declared sources have been modified on disk. Convention: wiki pages include YAML frontmatter with a 'sources' list of relative paths to raw source files. This tool checks whether those source files have changed since the page was last indexed. Output: list of {doc_path, title, stale_sources} where each stale source has a reason: 'modified', 'missing', or 'untracked'.

Wiki health dashboard. Returns: orphan pages (zero inbound internal links), most-linked pages (top 10), tag distribution, total internal link count, and sections-per-doc min/max/avg. Use for periodic wiki lint checks.

Per-tool latency analysis. window='session' reads the in-memory ring (last 512 calls per tool — always available); window='1h'|'24h'|'7d'|'all' reads the persistent SQLite sink at ~/.doc-index/telemetry.db (opt-in via JDOCMUNCH_PERF_TELEMETRY=1). Returns {window, telemetry_enabled, source, per_tool:{tool:{count,p50_ms,p95_ms,max_ms,errors,error_rate}}}.

Session self-monitor: returns {latency_per_tool, total_tokens_saved}. Lightweight; reads the in-memory latency ring + persistent savings counter. For windowed analysis use analyze_perf.

Doc-watcher coverage + login-service state. Reports whether the jdocmunch-watch background service is active and, per locally-indexed doc repo, whether its source_root still exists on disk (watchable). Returns {service, watchable_repo_count, local_repo_count, repos[], hint}. Run jdocmunch-mcp watch (foreground) or watch-install (login service) to keep indexes fresh on any on-disk doc change.

Finalize one canonical Markdown handoff for a completed documentation audit/analysis (jdocmunch.handoff/v1; suite parity with jCodeMunch). The server assembles YOUR sections deterministically, validates every evidence_refs entry against what this session actually retrieved (section ids or doc paths served by search_sections / search_titles / get_section / get_sections — unknown refs fail closed), persists the result session-scoped, and returns a compact receipt {handoff_id, resource_uri, sha256, length, canonical:true}. Read the immutable body via the munch://handoff/ resource; repeated reads are byte-identical. Appendices are included exactly once; no character limit; never writes to the documentation corpus.

Search fenced code blocks across the indexed docs by BM25 over the block content. Returns one row per block with {block_id, section_id, doc_path, title, lang, byte_start, byte_end, snippet, _score}. Optional lang filter (e.g. 'python', 'bash') and doc_path/path_glob scope filters (applied before scoring, same contract as search_sections). Use after index_local; requires INDEX_VERSION>=3.

Best-effort bridge from doc code blocks to jcodemunch code symbols. For each block, tokenizes identifiers and looks them up via jcodemunch's search_symbols. Returns {by_block, by_symbol, _meta} where _meta.bridge_available reports whether jcodemunch-mcp is importable.

Map a jdocmunch docs repo to candidate jCodeMunch code repo handles by source_root. The two suites use independent repo-identity models, so a docs handle (e.g. 'local/foo-docs') is NOT a valid jCodeMunch code_repo. Given a docs repo, returns candidates[{repo, confidence, reason, source_root}] (exact source_root match = high; containment = medium/low), an 'ambiguous' flag, and _meta.bridge_available. Use it to pick the right code_repo for the link_code_to_symbols / get_undocumented_symbols bridge tools.

Resolve a filesystem path (index root, subfolder, or file) to its indexed documentation repo handle via stored source_root metadata — O(1)-sized response, use instead of doc_list_repos when the path is known. Exact root match wins, then the most specific containing root; equally-specific duplicates return ambiguous:true with a bounded candidates list (max 5) plus total_matches. GitHub-indexed corpora (no source_root) never match. Read-only: never creates, refreshes, or deletes an index. Prefer absolute paths; relative paths resolve against the server CWD (echoed as _meta.resolved_path).

Find OpenAPI operations by path glob, method, and/or tag. All filters AND'd. Returns one row per match with {section_id, doc_path, method, path, operationId, summary, tags, deprecated}. Requires the spec to have been indexed under v1.18+ so structured metadata is present.

Return every operation whose tags list contains the given tag (exact). Convenience wrapper around find_endpoint with only a tag filter.

Return every operation whose request body or any response references the given schema. Each row gets a referenced_in list of all schema names that operation pulls in (so you can see the broader dependency cluster).

BFS walk of the schema reference graph from a root schema name. Returns {root, nodes:{name:{type, properties, required, refs}}, edges:[[from, to]], unresolved}. max_depth bounds the walk (default 5).

Glossary lookup. Returns every entry whose term equals the query (case-insensitive, exact). Glossary entries are extracted at index time from Term — definition Markdown patterns and RST .. glossary:: blocks.

List glossary terms in alphabetical order, optionally filtered by prefix. Capped at max_results (default 100).

v2.0+ related-section graph. Returns structural neighbors (siblings, children, parent, optional cousins) and semantic neighbors (top-N cosine over stored embeddings, score >= min_score). mode: structural | semantic | both.

Unified diff between the indexed snapshot and the current on-disk byte range for a section. Returns hashes + diff text; identical=true when the section is in sync with disk.

One-shot index health diagnostics. Returns section_count, doc_count, role_distribution, freshness counts, broken_link_count, drift status, BM25 corpus sanity, and embedding coverage.

Six-axis health radar for a doc repo: freshness, link_integrity, orphan_health, embedding_coverage, role_coverage, drift_health (omitted when no canary). Each axis is 0-100, plus composite + A-F grade. Pairs with diff_doc_health_radar for snapshot deltas. Mirrors jcm's and jData's health-radar shape — third leg of the suite-wide pattern.

Composite doc-PR risk profile. Fuses volume + blast_radius + backlink_burden + tutorial_disruption + role_weight signals over a caller-supplied list of changed sections into a 0-1 risk_score with risk_level (low/medium/high/critical), top-5 blockers, and a one-line recommended_action. Caller computes the change list from a git diff or pairs with get_recent_changes. Mirrors jcm's get_pr_risk_profile.

Diff two doc_health_radar payloads. Pure function — pass the radar sub-field from two doc_health_radar responses (e.g. yesterday vs today). Returns per-axis deltas, composite delta, grade change, regression and improvement lists (threshold: 3 points), one-line verdict.

Reconstruct an ordered tutorial chain starting from section_id. Detects frontmatter next:/prev: keys, inline 'Next:' / 'Previous:' markdown links, or ordered numeric filename prefixes (01-intro.md). Returns chain[] of {section_id, doc_path, title} plus the strategy used.

Best-effort inverse coverage: enumerate symbols in the jcodemunch code_repo and return those whose name (or qualified name) does not appear anywhere in this doc index. _meta.bridge_available=false when jcodemunch-mcp is not importable in this environment.

List defined repo groups (v1.26+). Each group is a named alias for a set of indexed repos that search_sections can fan out across via the repo_group kwarg.

Create, replace, or delete a repo group (v1.26+). Empty repos list deletes the group. Persisted to ~/.doc-index/_groups.jsonc (JSONC — hand-edits welcome).

Online weight tuning. Reads ranking_events from ~/.doc-index/telemetry.db (requires JDOCMUNCH_PERF_TELEMETRY=1) and proposes a per-repo semantic_weight step. dry_run=true skips the disk write. min_events gates against early overfitting. Learns from a recency window of the ledger (default 90 days) so stale events can't anchor the weights.

Byte-offset integrity check. Walks every section, byte-range-reads its current on-disk content, recomputes SHA-256, and compares to the stored content_hash. Reports drift / missing / error counts plus the drifting section ids. Sample N sections via the sample arg for cheap CI checks.

Embedding-drift canary. Without args, re-embeds the saved CANARY_STRINGS and reports per-canary cosine drift; alarm fires when max_drift > threshold (default 0.05 ≈ cosine<0.95). Pass capture=true to seed the snapshot first (idempotent unless force=true). Catches silent provider model upgrades that would otherwise corrupt index recall without changing dim.

Multi-signal section dedup detection. Fuses embedding cosine (when available) with title + body lexical Jaccard, clusters via union-find, ranks each cluster's canonical by backlink_count + size. Verdict tiers: near_duplicate, overlapping_topic, parallel_tutorial. Read-only.

Transitive impact of rewriting / restructuring a section. Walks the inbound reference graph to max_depth (default 3), classifies each hit as anchor / doc / tutorial, and returns direct_impact, transitive_impact, a summary, and a normalised blast_score in [0, 1]. Companion to get_backlinks (which is depth 1 only). Read-only.

Composite preflight: is this section safe to delete? Fuses tutorial-path membership, anchor-specific backlinks, transitive doc-level backlinks, and recent-edit recency into a single verdict (safe_to_delete, tutorial_path_blocking, anchor_referenced, backlinks_blocking, recently_edited_blocking) plus up to 5 ranked blockers and a one-line recommended_action. Read-only — never mutates the index.

Return the version-current CLAUDE.md / AGENT.md policy snippet for jdocmunch-mcp. Lets an agent keep a one-line CLAUDE.md (e.g. "Call jdocmunch_guide and strictly follow its instructions.") instead of pasting a static snippet that drifts from the installed version. Idempotent, no repo context required. Sibling of jcodemunch_guide.