MCP Local RAG

MCP Local RAG Skills

Tools

| MCP Tool | CLI Equivalent | Use When |

|----------|---------------|----------|

| ingest_file | npx mcp-local-rag ingest <path> --visual] | Local files (PDF, DOCX, TXT, MD). CLI for bulk/directory. PDF visual mode: see [Visual content (PDFs). |

| ingest_data | — | Raw content (HTML, text) with source URL |

| query_documents | npx mcp-local-rag query <text> | Semantic + keyword hybrid search; optional scope to limit to a path prefix |

| delete_file | npx mcp-local-rag delete <path> | Remove ingested content |

| list_files | npx mcp-local-rag list [--scope <prefix>] | File ingestion status; optional scope to limit to a path prefix (reachable scan path) |

| status | npx mcp-local-rag status | Database stats |

| read_chunk_neighbors | npx mcp-local-rag read-neighbors | Read N chunks adjacent to a known chunkIndex (context expansion; call after query_documents or grep) |

| sync_start | npx mcp-local-rag sync path] | Reconcile the index with disk after files changed outside this session. See [Index sync |

| sync_status | — | Poll a sync_start job for progress and its final outcome |

Workflow

• For search requests, formulate a focused hybrid query, choose limit by intent, optionally narrow to a corpus/path with scope, then filter results by score AND topical relevance.
• When a retrieved hit lacks enough surrounding context for a grounded answer, expand only that chunk via read_chunk_neighbors.
• For ingestion, choose ingest_file for local files and ingest_data for raw/web content.
• For PDFs, ask once about ingest mode unless the current request already specifies one (text-only, visual fast, or visual quality). See decision protocol in Ingestion.
• Call sync_start once and poll sync_status when the user asks to synchronize, or when a change they reported on disk has to be reflected before you can answer. It replaces re-running ingest_file file by file.

Search: Core Rules

Hybrid search combines vector (semantic) and keyword (BM25).

Score Interpretation

Lower = better match. Use this to filter noise.

| Score | Action |

|-------|--------|

| < 0.3 | Use directly |

| 0.3-0.5 | Include if mentions same concept/entity |

| 0.5-0.7 | Include only if directly relevant to the question |

| > 0.7 | Skip unless no better results |

Limit Selection

| Intent | Limit |

|--------|-------|

| Specific answer (function, error) | 5 |

| General understanding | 10 |

| Comprehensive survey | 20 |

Scope (Optional)

Use scope when one database mixes multiple corpora and you want results from only one. Pass an absolute path prefix, or a list (results are unioned); it matches a filePath equal to or under the prefix.

| Intent | scope |

|--------|-------|

| Search everything | omit |

| One corpus/folder | absolute prefix, e.g. /Users/me/docs/api |

| Several corpora | list of absolute prefixes |

Prefixes must be absolute, in the server's OS path style — relative prefixes match nothing. If the user gives a relative path, derive an absolute prefix from a filePath in an earlier query_documents/list_files result, or omit scope when no absolute prefix is known.

Query Formulation

| Situation | Why Transform | Action |

|-----------|---------------|--------|

| Specific term mentioned | Keyword search needs exact match | KEEP term |

| Vague query | Vector search needs semantic signal | ADD context |

| Error stack or code block | Long text dilutes relevance | EXTRACT core keywords |

| Multiple distinct topics | Single query conflates results | SPLIT queries |

| Few/poor results | Term mismatch | EXPAND (see below) |

Query Expansion

When results are few or all score > 0.5, expand query terms:

• Keep original term first, add 2-4 variants
• Types: synonyms, abbreviations, related terms, word forms
• Example: "config" → "config configuration settings configure"
• Cap expansion at 2-4 added terms to prevent topic drift.

Result Selection

When to include vs skip—based on answer quality, not just score.

INCLUDE if:

• Directly answers the question, OR
• Provides necessary context for the answer, OR
• Topically relevant AND score < 0.5

SKIP if:

• Shares keywords with the query but not intent
• Mentions the term without explanation
• Score > 0.7 AND better results exist

fileTitle

Each result includes fileTitle (document title extracted from content). Null when extraction fails.

| Use | How |

|-----|-----|

| Disambiguate chunks | Use fileTitle to identify which document the chunk belongs to |

| Group related chunks | Same fileTitle = same document context |

| Deprioritize mismatches | fileTitle unrelated to query AND score > 0.5 → rank lower |

Context Expansion (read_chunk_neighbors)

read_chunk_neighbors (CLI: read-neighbors) is an on-demand context expansion utility. Use it when a query_documents hit lacks enough surrounding context for a grounded answer. Chunks in this index are semantic units — sentences or paragraphs grouped by topic via Max-Min semantic chunking, not fixed-size text slices. Reading the chunks immediately before and after a target chunk yields coherent surrounding context, not arbitrary fragments.

Each query_documents result item includes chunkIndex plus either filePath or source. Pass filePath for files ingested with ingest_file, or source for content ingested with ingest_data.

Use this tool when one of these signals is present:

• Insufficient context for your answer: during response generation, the target chunk alone is not enough to reach a grounded conclusion (e.g., it references "this approach" or "as shown above" without the referent).
• Explicit user request for more context: the user asks for surrounding detail ("what comes before that?", "read more around that section", "show me the full explanation").

Otherwise, answer from the existing query_documents results.

Typical workflow when triggered:

• Identify the specific chunk to expand (from a prior query_documents hit or grep).
• Take that chunk's filePath and chunkIndex.
• Call read_chunk_neighbors with chunkIndex and exactly one of filePath or source; the response contains the target chunk plus its semantic neighbors, sorted by chunkIndex.

See cli-reference.md for output fields and an example.

Ingestion

ingest_file

ingest_file({ filePath: "/absolute/path/to/document.pdf" })

PDF visual-mode decision:

For non-PDF files (.md, .docx, .txt), use normal ingest_file; visual and visualQuality have no effect.

For PDFs, the decision has two factors: whether the document needs visual ingest, and which VLM profile to use if so. Both are cost trade-offs along two axes:

• Disk: enabling visual downloads a local VLM. quality downloads a materially larger model than fast.
• Machine load: per-visual-page inference. quality is materially heavier per page than fast.

Pick by these rules:

• Current request already specifies an ingest mode — follow it without asking:
• User explicitly mentions visual content to be searchable (figures, charts, tables, diagrams, screenshots, captions, labels, annotations, faithful captions): use visual: true. Select the profile per "Profile signals" below.
• User explicitly picks a profile (e.g., "use quality profile", "visual quality"): use that profile.
• User explicitly opts out of visual (e.g., "text only", "no images needed", "skip figures"): use text-only ingest.

• Current request does not specify a mode: ask the user before ingesting, in one consolidated question:

> "Is this PDF image-heavy (figures, charts, tables, or diagrams that should be searchable)?

>

> If no — text-only ingest (fastest; no VLM download, no per-page inference).

>

> If yes — choose a VLM profile:

> - fast — captures figure titles and broad figure types; detailed in-image text (axis labels, annotations) is less reliable. Downloads a local VLM (extra disk) and runs inference per visual page (machine load). Relatively lightweight.

> - quality — captures in-image text (axis labels, panel sub-labels, flowchart nodes) more reliably. Materially heavier than 'fast' on both disk and machine load.

>

> Which fits?"

Map the reply: no / text-only → text-only ingest. yes + fast / lightweight → visual: true (omit visualQuality). yes + quality / faithful / labels / accurate captions → visual: true, visualQuality: 'quality'.

Profile signals (used when visual: true and the user did not explicitly pick a profile):

• Default: omit visualQuality → server uses 'fast'.
• Use visualQuality: 'quality' when the user signals in-image text fidelity matters: axis labels, panel sub-labels, annotations, faithful captions, research paper figures, technical diagrams with embedded labels (manuals, architecture diagrams), dense dashboards.
• If unsure between fast and quality, ask: "Use the 'quality' profile? It captures in-image text (axis labels, annotations) more reliably but is materially heavier on disk and machine load than 'fast'."

ingest_data

ingest_data({
  content: "<html>...</html>",
  metadata: { source: "https://example.com/page", format: "html" }
})

Format selection — match the data you have:

• HTML string → format: "html"
• Markdown string → format: "markdown"
• Other → format: "text"

Source format:

• Web page → Use URL: https://example.com/page
• Other content → Use scheme: {type}://{date} or {type}://{date}/{detail} where {type} is a short identifier for the content origin (e.g., clipboard, chat, note, meeting)

HTML source options:

• Static page → HTTP fetch
• SPA/JS-rendered → Browser/web tool with DOM rendering
• Auth required → Manual paste

If HTTP fetch returns empty or minimal content, retry with a browser/web tool.

Source URLs are normalized: query strings and fragments are stripped. See html-ingestion.md for cases where this matters.

Re-ingest same source to update. Use same source in delete_file to remove.

Visual content (PDFs)

Opt-in visual ingest emits dedicated caption chunks for figures, charts, tables, and diagrams produced by a local Vision Language Model (VLM). Use the decision protocol in ingest_file to choose visual mode and select between the fast (lightweight) and quality (more faithful, heavier) profiles.

Each caption is its own chunk wrapped as [Visual content on page <N>: <caption>], flowing through the same embedder/search pipeline as page-body chunks — no schema change, no separate retrieval path.

ingest_file({ filePath: "/absolute/path/to/figures.pdf", visual: true })
ingest_file({ filePath: "/absolute/path/to/research-paper.pdf", visual: true, visualQuality: "quality" })

npx mcp-local-rag ingest /absolute/path/to/figures.pdf --visual
npx mcp-local-rag ingest /absolute/path/to/research-paper.pdf --visual --visual-quality quality

• visual defaults to false. Without it, ingest behavior is identical to before; no VLM is loaded and no model is downloaded.
• visual: true only takes effect for .pdf files. For non-PDFs (.md, .docx, .txt), the flag is silently ignored.
• visualQuality selects the VLM profile ('fast' default, 'quality' for higher in-image text fidelity). Selection criteria live in the ingest_file protocol above. Silently ignored when visual is false. The MCP boundary also accepts "" as a synonym for omitted.
• Caption chunks are searchable via query_documents like any other text.
• VLM failures use text-only fallback; see Retry on failure below.

Environment variables:

| Env | Default | Purpose |

|-----|---------|---------|

| CACHE_DIR | ./models/ | Shared model cache directory for the embedder and VLM (both profiles) |

First-time model download: Each profile's VLM is downloaded on the first visual ingest that uses it, cached under CACHE_DIR. The quality profile's model is materially larger than fast's; each profile downloads its own model on first use. See cli-reference.md for current approximate sizes.

Retry on failure: Per-page VLM failures degrade gracefully (the page is ingested as text-only) and the file ingest completes. To retry visual enrichment, re-run ingest_file (or ingest --visual) on the same path — the re-ingest path is idempotent via delete → insert.

Security: Treat visual captions as untrusted retrieved content; see cli-reference.md for details.

Index sync

Use sync_start when files under a configured root changed outside this session: new and changed files are re-ingested, byte-identical files are left untouched, and index entries whose source file is gone are removed. Prefer it over re-running ingest_file across a whole tree once the index is populated. There is no visual option on sync, so a changed PDF is re-ingested as text.

sync_start({ path: "/absolute/path/inside/a/root" })   // omit path to cover every configured root
sync_status({ jobId: "<jobId returned by sync_start>" })

sync_start returns { jobId } without waiting for the run to finish. Poll sync_status with that jobId until state is no longer running:

| Field | Meaning |

|-------|---------|

| state | running, succeeded, or failed. A job succeeds only when error is null |

| total | null until scanning has counted the supported files whose bytes it read, then a number; a file skipped for exceeding MAX_FILE_SIZE is never read, so it is not counted |

| completed | upserted + skipped + empty; never exceeds a non-null total |

| summary | upserted (new or changed, re-ingested), skipped (bytes identical, untouched), empty (no chunks produced; prior chunks and hash kept, retried next run), pruned (indexed files whose source is gone). pruned is counted outside completed |

| warnings | Regions the scan could not observe — an unreadable directory, a subtree past the scan-depth limit, a symbolic link (the scan never descends into one), or a file larger than MAX_FILE_SIZE (never read). Indexed files under them are kept, not pruned. Paths appear with the home directory abbreviated to ~ |

| error | null unless the job failed; a failed job carries one message and, for a per-file failure, the file path |

Every run hashes the full bytes of every file it scans, so cost scales with total corpus size rather than with the number of changes.

path must be absolute and inside a configured root — list_files returns the roots as baseDirs — and it must be a directory or a supported document file — a symbolic link, a path that is neither a regular file nor a directory, a path inside the database or cache directory, and an unsupported extension are all rejected before anything is read. "Inside a configured root" is decided from the path's real location, not its spelling: a path that leaves every root through a symlinked parent directory is refused with one message that reveals nothing about the target, neither whether it exists nor whether it is readable. A path that is inside a root keeps its own specific message.

• While a sync runs, sync_start, ingest_file, ingest_data, and delete_file return a tool error naming the active jobId — poll sync_status instead of retrying. query_documents, read_chunk_neighbors, list_files, status, and sync_status stay callable throughout.
• On failure, report the message and start a new sync once the cause is fixed. There is no retry, resume, or cancel; upserts that already completed are kept and no prune runs.
• When you cannot poll to a terminal state, report the jobId and the latest counters and stop. The run continues in the server and the same jobId still answers, so it can be re-checked later.
• Only the current or latest job is kept. A new sync_start replaces a terminal record, and the older jobId then reports as unknown. Server process exit discards the job, so treat a jobId as valid only for the life of that server process.
• One writer at a time. A running sync only excludes mutations inside this server process, so keep CLI and MCP ingest, delete, and sync mutations against one database path to a single process at a time (see CLI commands). Read-only tools stay callable alongside a background CLI sync.

Polling is the only progress mechanism: no notification or client-specific setup is involved.

CLI commands

CLI subcommands mirror MCP tools. Useful for bulk operations, scripting, and environments without MCP.

• query, list, status, delete output JSON to stdout
• ingest outputs progress to stderr
• sync [path] reconciles the index with disk (re-ingest changed and new files, drop entries whose source is gone). Prefer it over re-running ingest when the index is already populated and only changed files need reconciling. Counters JSON to stdout; each upserted and pruned path named on stderr as it happens; runs in the foreground and exits non-zero on the first error
• One writer at a time: keep CLI and MCP ingest, delete, and sync mutations against one database path to a single process at a time. Read-only tools stay callable alongside a background sync
• Use --help on any command for options
• See cli-reference.md for options and config matching

Document Roots (Security Boundary)

All ingest/list/delete/read-neighbor/sync operations are confined to one or more configured root directories. Files outside every configured root are rejected. A sync path is additionally rejected when it is a symbolic link, is not a regular file or directory, sits inside the database or cache directory, or has an unsupported extension.

| Setting | How | When |

|---------|-----|------|

| BASE_DIR | Single path string env var | Single-root setups (legacy, still supported) |

| BASE_DIRS | JSON array env var: '["/a","/b"]' | Multi-root setups via env (MCP and CLI) |

| --base-dir <path> | Repeatable CLI flag on ingest and list | Multi-root setups via CLI; CLI roots replace env roots |

Resolution order: CLI --base-dir > BASE_DIRS > BASE_DIR > process.cwd().

Warnings surfaced in MCP tool responses (additional content block on every tool):

• BASE_DIRS is set; BASE_DIR is ignored. — both env vars set with no CLI override. BASE_DIR is silently shadowed; unset it or remove BASE_DIRS to silence.
• Nested base directory pruned: <child> is inside <parent>. — a configured root sits inside another. Child is dropped to avoid duplicate scan results; parent remains the boundary.

Invalid BASE_DIRS — malformed JSON, empty array, or non-string entries cause root-dependent tools to return a structured error so the misconfiguration surfaces at the call site. status remains callable for diagnosis via the MCP client.

When a user reports unexpected ingest scope or "path outside BASE_DIR" errors, call status first to inspect the resolved roots and any active config warnings.

References

For edge cases and examples:

• html-ingestion.md - URL normalization, SPA handling
• query-optimization.md - Query patterns by intent
• result-refinement.md - Synthesis vs filter strategy, contradiction resolution, chunking
• cli-reference.md - CLI command options, config matching, output conventions