@nacho-labs/mcp-semantic-search 0.3.3 → 0.5.0

package/README.md

@@ -10,7 +10,7 @@ no API keys, no cloud, no costs.
 ## Prerequisites
 
 - **Node.js 20.9+**
-- **Internet on first run** to download the embedding model (~25MB, cached permanently)
+- **Internet on first run** to download the embedding model (~25MB, cached in a per-user directory)
 
 ## Quick start
 
@@ -103,12 +103,32 @@ npx @nacho-labs/mcp-semantic-search \
 
 ### Environment variables
 
-| Variable                  | Description                    | Default                   |
-| ------------------------- | ------------------------------ | ------------------------- |
-| `MCP_SEMANTIC_STORE`      | Path to persistence file       | `.semantic-store.json`    |
-| `MCP_SEMANTIC_SIMILARITY` | Min similarity threshold (0-1) | `0.4`                     |
-| `MCP_SEMANTIC_MODEL`      | Embedding model                | `Xenova/all-MiniLM-L6-v2` |
-| `MCP_SEMANTIC_CACHE_DIR`  | Model cache directory          | `.cache/transformers`     |
+| Variable                              | Description                                                                    | Default                    |
+| ------------------------------------- | ------------------------------------------------------------------------------ | -------------------------- |
+| `MCP_SEMANTIC_STORE`                  | Path to persistence file                                                       | `.semantic-store.json`     |
+| `MCP_SEMANTIC_SIMILARITY`             | Min similarity threshold (0-1)                                                 | `0.4`                      |
+| `MCP_SEMANTIC_MODEL`                  | Embedding model                                                                | `Xenova/all-MiniLM-L6-v2`  |
+| `MCP_SEMANTIC_CACHE_DIR`              | Model cache directory                                                          | per-user cache (see below) |
+| `MCP_SEMANTIC_ON_CORRUPT_STORE`       | `throw` or `quarantine` when the store file is corrupt                         | `throw`                    |
+| `MCP_SEMANTIC_DEDUPLICATE_EXACT`      | Exact-duplicate detection (maps to `deduplicate: 'normalized'`)                | `true`                     |
+| `MCP_SEMANTIC_DEDUPLICATE_SIMILARITY` | Near-duplicate threshold; `> 0` takes precedence over exact (`{ similarity }`) | `0.95`                     |
+
+Both dedup settings off (`false` and `0`) disables deduplication.
+
+### Model cache
+
+Unless `MCP_SEMANTIC_CACHE_DIR` is set, models are cached per user and shared
+across projects: `$NACHOS_EMBEDDINGS_CACHE`, else the XDG cache directory, else
+`~/.cache/nachos-embeddings`. Earlier versions used `.cache/transformers` in the
+working directory; set `MCP_SEMANTIC_CACHE_DIR` to that path to keep using an
+existing cache instead of re-downloading (~90MB).
+
+### Corrupt store
+
+If the store file cannot be parsed, the server exits with a non-zero status and
+a message naming the file; it does not retry. Repair or delete the file, or set
+`MCP_SEMANTIC_ON_CORRUPT_STORE=quarantine` to rename the corrupt file aside and
+start with an empty index.
 
 ### With environment variables in MCP config
 

package/dist/config.d.ts

@@ -0,0 +1,30 @@
+export type DeduplicateOption = 'off' | 'exact' | 'normalized' | {
+    similarity: number;
+};
+export type CorruptStoreMode = 'throw' | 'quarantine';
+/**
+ * Map the legacy exact/similarity settings onto nachos-embeddings' `deduplicate` option.
+ * similarity > 0 wins; otherwise exact on means 'normalized'; both off means 'off'.
+ */
+export declare function resolveDeduplicate(exact: boolean, similarity: number): DeduplicateOption;
+export declare function parseCorruptStoreMode(value: string): CorruptStoreMode;
+export declare function getConfig(argv?: string[], env?: NodeJS.ProcessEnv): {
+    storePath: string;
+    minSimilarity: number;
+    model: string;
+    cacheDir: string | undefined;
+    autoChunk: boolean;
+    deduplicateExact: boolean;
+    deduplicateSimilarity: number;
+    deduplicate: DeduplicateOption;
+    onCorruptStore: CorruptStoreMode;
+    temporalBoost: boolean;
+    verbose: boolean;
+    provider: 'transformers' | 'bedrock';
+    bedrockRegion: string;
+    bedrockModel: string;
+    bedrockProfile: string;
+    bedrockDimensions: number;
+};
+export type Config = ReturnType<typeof getConfig>;
+//# sourceMappingURL=config.d.ts.map

package/dist/config.d.ts.map

@@ -0,0 +1 @@
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package/dist/config.js

@@ -0,0 +1,52 @@
+/**
+ * Map the legacy exact/similarity settings onto nachos-embeddings' `deduplicate` option.
+ * similarity > 0 wins; otherwise exact on means 'normalized'; both off means 'off'.
+ */
+export function resolveDeduplicate(exact, similarity) {
+    if (Number.isFinite(similarity) && similarity > 0)
+        return { similarity };
+    return exact ? 'normalized' : 'off';
+}
+export function parseCorruptStoreMode(value) {
+    if (value === 'throw' || value === 'quarantine')
+        return value;
+    throw new Error(`Invalid MCP_SEMANTIC_ON_CORRUPT_STORE "${value}". Expected "throw" or "quarantine".`);
+}
+export function getConfig(argv = process.argv.slice(2), env = process.env) {
+    function getArg(name, fallback) {
+        const idx = argv.indexOf(`--${name}`);
+        return idx !== -1 && idx + 1 < argv.length ? argv[idx + 1] : fallback;
+    }
+    function getString(name, fallback) {
+        const envName = `MCP_SEMANTIC_${name.toUpperCase().replace(/-/g, '_')}`;
+        return env[envName] ?? getArg(name, fallback);
+    }
+    function getBool(name, fallback) {
+        const value = getString(name, fallback.toString());
+        return value === 'true' || value === '1';
+    }
+    const deduplicateExact = getBool('deduplicate-exact', true);
+    const deduplicateSimilarity = parseFloat(getString('deduplicate-similarity', '0.95'));
+    // Empty means "use the library's per-user cache".
+    const cacheDir = getString('cache-dir', '');
+    return {
+        storePath: getString('store', '.semantic-store.json'),
+        minSimilarity: parseFloat(getString('similarity', '0.4')),
+        model: getString('model', 'Xenova/all-MiniLM-L6-v2'),
+        cacheDir: cacheDir === '' ? undefined : cacheDir,
+        autoChunk: getBool('auto-chunk', true),
+        deduplicateExact,
+        deduplicateSimilarity,
+        deduplicate: resolveDeduplicate(deduplicateExact, deduplicateSimilarity),
+        onCorruptStore: parseCorruptStoreMode(getString('on-corrupt-store', 'throw')),
+        temporalBoost: getBool('temporal-boost', true),
+        verbose: getBool('verbose', false),
+        // Bedrock provider settings
+        provider: getString('provider', 'transformers'),
+        bedrockRegion: getString('bedrock-region', 'us-east-1'),
+        bedrockModel: getString('bedrock-model', 'amazon.titan-embed-text-v2:0'),
+        bedrockProfile: getString('bedrock-profile', ''),
+        bedrockDimensions: parseInt(getString('bedrock-dimensions', '1024'), 10),
+    };
+}
+//# sourceMappingURL=config.js.map

package/dist/config.js.map

@@ -0,0 +1 @@
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package/dist/index.js

@@ -1,10 +1,15 @@
 #!/usr/bin/env node
 import { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
 import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
+import { ErrorCode, ListResourcesRequestSchema, ListResourceTemplatesRequestSchema, McpError, ReadResourceRequestSchema, } from '@modelcontextprotocol/sdk/types.js';
 import { z } from 'zod';
-import { EnhancedSemanticSearch } from '@nacho-labs/nachos-embeddings';
+import { SemanticSearch } from '@nacho-labs/nachos-embeddings';
 import { resolve } from 'node:path';
-const VERSION = '0.3.2';
+import { getConfig } from './config.js';
+import { initWithRetry } from './init.js';
+import { OpQueue } from './op-queue.js';
+import { DEFAULT_INDEX_ID, DOCUMENT_RESOURCE_TEMPLATE_URI, INDEX_MANIFEST_URI, INDEX_STATS_URI, REGISTERED_RESOURCE_URIS, buildDocumentResourceUri, } from './product.js';
+const VERSION = '0.5.0';
 const MAX_LENGTH = 1_000_000;
 const MAX_ITEMS = 100;
 const metadataValueSchema = z.union([
@@ -13,38 +18,6 @@ const metadataValueSchema = z.union([
     z.boolean(),
     z.array(z.string().max(MAX_LENGTH)).max(MAX_ITEMS),
 ]);
-function getConfig() {
-    const args = process.argv.slice(2);
-    function getArg(name, fallback) {
-        const idx = args.indexOf(`--${name}`);
-        return idx !== -1 && idx + 1 < args.length ? args[idx + 1] : fallback;
-    }
-    function getString(name, fallback) {
-        const envName = `MCP_SEMANTIC_${name.toUpperCase().replace(/-/g, '_')}`;
-        return process.env[envName] ?? getArg(name, fallback);
-    }
-    function getBool(name, fallback) {
-        const value = getString(name, fallback.toString());
-        return value === 'true' || value === '1';
-    }
-    return {
-        storePath: resolve(getString('store', '.semantic-store.json')),
-        minSimilarity: parseFloat(getString('similarity', '0.4')),
-        model: getString('model', 'Xenova/all-MiniLM-L6-v2'),
-        cacheDir: getString('cache-dir', '.cache/transformers'),
-        autoChunk: getBool('auto-chunk', true),
-        deduplicateExact: getBool('deduplicate-exact', true),
-        deduplicateSimilarity: parseFloat(getString('deduplicate-similarity', '0.95')),
-        temporalBoost: getBool('temporal-boost', true),
-        verbose: getBool('verbose', false),
-        // Bedrock provider settings
-        provider: getString('provider', 'transformers'),
-        bedrockRegion: getString('bedrock-region', 'us-east-1'),
-        bedrockModel: getString('bedrock-model', 'amazon.titan-embed-text-v2:0'),
-        bedrockProfile: getString('bedrock-profile', ''),
-        bedrockDimensions: parseInt(getString('bedrock-dimensions', '1024'), 10),
-    };
-}
 async function createProvider(config) {
     if (config.provider !== 'bedrock') {
         return undefined; // Use default Transformers.js
@@ -58,7 +31,15 @@ async function createProvider(config) {
         progressLogging: config.verbose,
     });
 }
-const config = getConfig();
+let config;
+try {
+    config = getConfig();
+}
+catch (err) {
+    console.error(err instanceof Error ? err.message : String(err));
+    process.exit(1);
+}
+config.storePath = resolve(config.storePath);
 const metrics = {
     searches: 0,
     documentsAdded: 0,
@@ -67,49 +48,21 @@ const metrics = {
     startTime: Date.now(),
 };
 const provider = await createProvider(config);
-const search = new EnhancedSemanticSearch({
+const search = new SemanticSearch({
     ...(provider ? { provider } : {}),
     minSimilarity: config.minSimilarity,
     model: config.model,
-    cacheDir: config.cacheDir,
+    ...(config.cacheDir ? { cacheDir: config.cacheDir } : {}),
     autoSave: true,
     storePath: config.storePath,
     autoChunk: config.autoChunk,
-    deduplicateExact: config.deduplicateExact,
-    deduplicateSimilarity: config.deduplicateSimilarity,
+    deduplicate: config.deduplicate,
+    onCorruptStore: config.onCorruptStore,
     temporalBoost: config.temporalBoost,
     verbose: config.verbose,
 });
-async function initializeSearch(attempt, maxRetries) {
-    if (config.verbose) {
-        console.error(`[Init] Attempt ${attempt}/${maxRetries}`);
-    }
-    await search.init();
-    if (config.verbose) {
-        console.error(`[Init] Loaded ${search.size()} documents`);
-    }
-}
-async function handleInitializationFailure(attempt, maxRetries, err) {
-    if (attempt === maxRetries) {
-        console.error('[Init] Failed after', maxRetries, 'attempts. Internet required on first run (~25MB download).', err);
-        throw err;
-    }
-    console.error(`[Init] Retry in 2s...`, err);
-    await new Promise((resolve) => setTimeout(resolve, 2000));
-}
-async function initWithRetry(maxRetries = 3) {
-    for (let attempt = 1; attempt <= maxRetries; attempt++) {
-        try {
-            await initializeSearch(attempt, maxRetries);
-            return;
-        }
-        catch (err) {
-            await handleInitializationFailure(attempt, maxRetries, err);
-        }
-    }
-}
 try {
-    await initWithRetry();
+    await initWithRetry({ search, storePath: config.storePath, verbose: config.verbose });
 }
 catch {
     process.exit(1);
@@ -123,85 +76,195 @@ function formatUptime(seconds) {
     }
     return `${Math.floor(seconds / 3600)}h ${Math.floor((seconds % 3600) / 60)}m`;
 }
-function matchesKind(meta, kind) {
-    return !kind || meta?.kind === kind;
+const opQueue = new OpQueue(() => {
+    metrics.errors++;
+});
+const server = new McpServer({ name: 'mcp-semantic-search-enhanced', version: VERSION }, { capabilities: { logging: {} } });
+function getResourceDocuments() {
+    return search.export();
 }
-function matchesTags(meta, tags) {
-    return !tags || Boolean(meta?.tags && tags.some((tag) => meta.tags?.includes(tag)));
+function getResourceModelLabel() {
+    return config.provider === 'bedrock' ? config.bedrockModel : config.model;
 }
-function hasValidSince(parsedSince) {
-    return parsedSince !== undefined && !isNaN(parsedSince);
+function getLatestDocumentTimestamp(documents) {
+    const latest = documents.reduce((current, document) => {
+        const timestamp = document.metadata?.timestamp;
+        return timestamp !== undefined && (current === undefined || timestamp > current) ? timestamp : current;
+    }, undefined);
+    return latest === undefined || Number.isNaN(latest) ? undefined : new Date(latest).toISOString();
 }
-function isBeforeSince(meta, parsedSince) {
-    return Boolean(meta?.timestamp && meta.timestamp < parsedSince);
+function countMetadata(documents, key) {
+    const counts = {};
+    for (const document of documents) {
+        const values = key === 'tags' ? (document.metadata?.tags ?? []) : document.metadata?.kind ? [document.metadata.kind] : [];
+        for (const value of values)
+            counts[value] = (counts[value] ?? 0) + 1;
+    }
+    return counts;
 }
-function matchesSince(meta, parsedSince) {
-    return !hasValidSince(parsedSince) || !isBeforeSince(meta, parsedSince);
+function renderJsonResource(uri, value) {
+    return {
+        contents: [{ uri, mimeType: 'application/json', text: JSON.stringify(value, null, 2) }],
+    };
 }
-function matchesMetadata(meta, kind, tags, parsedSince) {
-    return matchesKind(meta, kind) && matchesTags(meta, tags) && matchesSince(meta, parsedSince);
+function formatSearchResults(results) {
+    return results
+        .map((r, i) => {
+        const preview = r.text.substring(0, 200) + (r.text.length > 200 ? '...' : '');
+        const metaStr = r.metadata && Object.keys(r.metadata).length > 0 ? `\n   📎 ${JSON.stringify(r.metadata)}` : '';
+        return `${i + 1}. [${(r.similarity * 100).toFixed(0)}%] ${preview}${metaStr}`;
+    })
+        .join('\n\n');
 }
-class OpQueue {
-    queue = Promise.resolve();
-    async run(fn) {
-        const prev = this.queue;
-        let resolve;
-        this.queue = new Promise((res) => {
-            resolve = res;
-        });
-        try {
-            await prev.catch(() => { });
-            const result = await fn();
-            return result;
-        }
-        catch (err) {
-            metrics.errors++;
-            throw err;
-        }
-        finally {
-            resolve();
-        }
+function parseSemanticResourceUri(uri) {
+    try {
+        const parsed = new URL(uri);
+        if (parsed.protocol !== 'semantic-search:' || parsed.hostname !== 'indexes')
+            return undefined;
+        const [indexId, resourceType, documentId, extra] = parsed.pathname
+            .split('/')
+            .filter(Boolean)
+            .map((segment) => decodeURIComponent(segment));
+        if (indexId !== DEFAULT_INDEX_ID || extra !== undefined)
+            return undefined;
+        if (resourceType === 'manifest' && documentId === undefined)
+            return { type: 'manifest' };
+        if (resourceType === 'stats' && documentId === undefined)
+            return { type: 'stats' };
+        if (resourceType === 'documents' && documentId)
+            return { type: 'document', documentId };
+    }
+    catch {
+        return undefined;
     }
+    return undefined;
 }
-const opQueue = new OpQueue();
-const server = new McpServer({ name: 'mcp-semantic-search-enhanced', version: VERSION }, { capabilities: { logging: {} } });
-function buildHealthResponse() {
-    const uptime = Math.floor((Date.now() - metrics.startTime) / 1000);
-    const model = config.provider === 'bedrock' ? config.bedrockModel : config.model;
-    const providerSetting = config.provider === 'bedrock' ? `Region: ${config.bedrockRegion}` : `Cache: ${config.cacheDir}`;
+server.server.registerCapabilities({ resources: {} });
+server.server.setRequestHandler(ListResourcesRequestSchema, async () => {
+    const documents = getResourceDocuments();
+    const lastModified = getLatestDocumentTimestamp(documents);
+    const annotations = {
+        audience: ['user', 'assistant'],
+        ...(lastModified ? { lastModified } : {}),
+    };
     return {
-        content: [
+        resources: [
+            {
+                uri: INDEX_MANIFEST_URI,
+                name: 'semantic_index_manifest',
+                title: 'Semantic Index Manifest',
+                description: 'Stable manifest for the active semantic-search index.',
+                mimeType: 'application/json',
+                annotations: { ...annotations, priority: 1 },
+            },
             {
-                type: 'text',
-                text: [
-                    '✅ Healthy',
-                    '',
-                    '📊 Metrics:',
-                    `   Documents: ${search.size()}`,
-                    `   Searches: ${metrics.searches}`,
-                    `   Added: ${metrics.documentsAdded}`,
-                    `   Removed: ${metrics.documentsRemoved}`,
-                    `   Errors: ${metrics.errors}`,
-                    `   Uptime: ${formatUptime(uptime)}`,
-                    '',
-                    '⚙️ Config:',
-                    `   Provider: ${config.provider}`,
-                    `   Model: ${model}`,
-                    `   ${providerSetting}`,
-                    `   Store: ${config.storePath}`,
-                    `   Min similarity: ${config.minSimilarity}`,
-                    `   Auto-chunk: ${config.autoChunk}`,
-                    `   Dedup: exact=${config.deduplicateExact}, fuzzy=${config.deduplicateSimilarity}`,
-                    `   Temporal boost: ${config.temporalBoost}`,
-                ].join('\n'),
+                uri: INDEX_STATS_URI,
+                name: 'semantic_index_stats',
+                title: 'Semantic Index Stats',
+                description: 'Corpus stats and runtime counters for the active semantic-search index.',
+                mimeType: 'application/json',
+                annotations: { ...annotations, priority: 0.9 },
             },
         ],
     };
-}
-async function getHealthResponse() {
+});
+server.server.setRequestHandler(ListResourceTemplatesRequestSchema, async () => ({
+    resourceTemplates: [
+        {
+            name: 'semantic_document',
+            title: 'Indexed Document',
+            uriTemplate: DOCUMENT_RESOURCE_TEMPLATE_URI,
+            description: 'Read a single indexed document by id from the active semantic-search index.',
+            mimeType: 'application/json',
+            annotations: { audience: ['user', 'assistant'], priority: 0.8 },
+        },
+    ],
+}));
+server.server.setRequestHandler(ReadResourceRequestSchema, async (request) => {
+    const resource = parseSemanticResourceUri(request.params.uri);
+    if (!resource)
+        throw new McpError(ErrorCode.InvalidParams, `Resource ${request.params.uri} not found`);
+    const documents = getResourceDocuments();
+    if (resource.type === 'manifest') {
+        return renderJsonResource(INDEX_MANIFEST_URI, {
+            indexId: DEFAULT_INDEX_ID,
+            resourceRoot: `semantic-search://indexes/${DEFAULT_INDEX_ID}`,
+            storePath: config.storePath,
+            provider: config.provider,
+            model: getResourceModelLabel(),
+            documentCount: documents.length,
+            listedResources: [...REGISTERED_RESOURCE_URIS],
+            resourceTemplates: [DOCUMENT_RESOURCE_TEMPLATE_URI],
+            metricsStartedAt: new Date(metrics.startTime).toISOString(),
+        });
+    }
+    if (resource.type === 'stats') {
+        return renderJsonResource(INDEX_STATS_URI, {
+            indexId: DEFAULT_INDEX_ID,
+            storePath: config.storePath,
+            provider: config.provider,
+            model: getResourceModelLabel(),
+            counts: {
+                documents: documents.length,
+                rootDocuments: documents.filter((document) => !document.metadata?.parentId).length,
+                chunkDocuments: documents.filter((document) => document.metadata?.parentId).length,
+            },
+            metadata: { kinds: countMetadata(documents, 'kind'), tags: countMetadata(documents, 'tags') },
+            usage: {
+                searches: metrics.searches,
+                documentsAdded: metrics.documentsAdded,
+                documentsRemoved: metrics.documentsRemoved,
+                errors: metrics.errors,
+                uptimeSeconds: Math.floor((Date.now() - metrics.startTime) / 1000),
+            },
+        });
+    }
+    const document = documents.find((candidate) => candidate.id === resource.documentId);
+    if (!document)
+        throw new McpError(ErrorCode.InvalidParams, `Document ${resource.documentId} not found`);
+    return renderJsonResource(buildDocumentResourceUri(document.id), {
+        id: document.id,
+        text: document.text,
+        metadata: document.metadata ?? {},
+    });
+});
+server.registerTool('semantic_health', {
+    title: 'Health Check',
+    description: 'Server status, metrics, and configuration',
+    inputSchema: z.object({}),
+}, async () => {
     try {
         await search.search('test', { limit: 1 });
-        return buildHealthResponse();
+        const uptime = Math.floor((Date.now() - metrics.startTime) / 1000);
+        const uptimeStr = formatUptime(uptime);
+        return {
+            content: [
+                {
+                    type: 'text',
+                    text: [
+                        '✅ Healthy',
+                        '',
+                        '📊 Metrics:',
+                        `   Documents: ${search.size()}`,
+                        `   Searches: ${metrics.searches}`,
+                        `   Added: ${metrics.documentsAdded}`,
+                        `   Removed: ${metrics.documentsRemoved}`,
+                        `   Errors: ${metrics.errors}`,
+                        `   Uptime: ${uptimeStr}`,
+                        '',
+                        '⚙️ Config:',
+                        `   Provider: ${config.provider}`,
+                        `   Model: ${config.provider === 'bedrock' ? config.bedrockModel : config.model}`,
+                        `   ${config.provider === 'bedrock' ? `Region: ${config.bedrockRegion}` : `Cache: ${config.cacheDir ?? 'library default (per-user)'}`}`,
+                        `   Store: ${config.storePath}`,
+                        `   Min similarity: ${config.minSimilarity}`,
+                        `   Auto-chunk: ${config.autoChunk}`,
+                        `   Dedup: ${JSON.stringify(config.deduplicate)}`,
+                        `   Temporal boost: ${config.temporalBoost}`,
+                    ].join('\n'),
+                },
+            ],
+        };
     }
     catch (err) {
         return {
@@ -213,19 +276,14 @@ async function getHealthResponse() {
             ],
         };
     }
-}
-server.registerTool('semantic_health', {
-    title: 'Health Check',
-    description: 'Server status, metrics, and configuration',
-    inputSchema: z.object({}),
-}, getHealthResponse);
+});
 server.registerTool('semantic_search', {
     title: 'Semantic Search',
     description: 'Search by meaning with optional metadata filters',
     inputSchema: z.object({
         query: z.string().describe('Search query'),
-        limit: z.number().optional().default(5).describe('Max results'),
-        minSimilarity: z.number().optional().describe('Min score (0-1)'),
+        limit: z.number().int().min(1).max(100).optional().default(5).describe('Max results'),
+        minSimilarity: z.number().min(0).max(1).optional().describe('Min score (0-1)'),
         kind: z.string().optional().describe('Filter by metadata.kind'),
         tags: z.array(z.string()).optional().describe('Filter by metadata.tags'),
         since: z.string().optional().describe('Filter by metadata.timestamp >= ISO date'),
@@ -234,10 +292,19 @@ server.registerTool('semantic_search', {
     return opQueue.run(async () => {
         const startTime = Date.now();
         const parsedSince = since ? Date.parse(since) : undefined;
+        const targetTags = tags ? new Set(tags) : undefined;
         const results = await search.search(query, {
             limit,
             ...(minSimilarity !== undefined && { minSimilarity }),
-            filter: (meta) => matchesMetadata(meta, kind, tags, parsedSince),
+            filter: (meta) => {
+                if (kind && meta?.kind !== kind)
+                    return false;
+                if (targetTags && (!meta?.tags || !meta.tags.some((t) => targetTags.has(t))))
+                    return false;
+                if (parsedSince !== undefined && !isNaN(parsedSince) && meta?.timestamp && meta.timestamp < parsedSince)
+                    return false;
+                return true;
+            },
         });
         metrics.searches++;
         const elapsed = Date.now() - startTime;
@@ -251,19 +318,20 @@ server.registerTool('semantic_search', {
                 ],
             };
         }
-        const formatted = results
-            .map((r, i) => {
-            const preview = r.text.substring(0, 200) + (r.text.length > 200 ? '...' : '');
-            const metaStr = r.metadata && Object.keys(r.metadata).length > 0 ? `\n   📎 ${JSON.stringify(r.metadata)}` : '';
-            return `${i + 1}. [${(r.similarity * 100).toFixed(0)}%] ${preview}${metaStr}`;
-        })
-            .join('\n\n');
+        const formatted = formatSearchResults(results);
         return {
             content: [
                 {
                     type: 'text',
                     text: `🔍 Found ${results.length} in ${elapsed}ms:\n\n${formatted}`,
                 },
+                ...results.map((result) => ({
+                    type: 'resource_link',
+                    uri: buildDocumentResourceUri(result.id),
+                    name: result.id,
+                    mimeType: 'application/json',
+                    description: `Indexed document "${result.id}"`,
+                })),
             ],
         };
     });
@@ -312,7 +380,7 @@ server.registerTool('semantic_index_batch', {
 }, async ({ documents }) => {
     return opQueue.run(async () => {
         const startTime = Date.now();
-        await search.addDocuments(documents.map((d) => ({ ...d, metadata: d.metadata })));
+        await search.addDocuments(documents);
         metrics.documentsAdded += documents.length;
         const elapsed = Date.now() - startTime;
         return {
@@ -370,8 +438,7 @@ server.registerTool('semantic_stats', {
                 '',
                 'Features:',
                 `   Auto-chunk: ${config.autoChunk}`,
-                `   Dedup (exact): ${config.deduplicateExact}`,
-                `   Dedup (fuzzy): ${config.deduplicateSimilarity > 0 ? config.deduplicateSimilarity : 'off'}`,
+                `   Dedup: ${JSON.stringify(config.deduplicate)}`,
                 `   Temporal boost: ${config.temporalBoost}`,
                 '',
                 'Usage:',

package/dist/index.js.map

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package/dist/init.d.ts

@@ -0,0 +1,23 @@
+export declare function isStoreCorruptError(err: unknown): err is Error & {
+    path?: string;
+};
+export interface InitDeps {
+    search: {
+        init(): Promise<void>;
+        size(): number;
+    };
+    storePath: string;
+    verbose: boolean;
+    maxRetries?: number;
+    retryDelayMs?: number;
+    log?: (...args: unknown[]) => void;
+}
+export declare function corruptStoreMessage(err: Error & {
+    path?: string;
+}, storePath: string): string;
+/**
+ * Initialise the search index. Corrupt stores are never retried. Throws on final failure
+ * after logging an actionable message.
+ */
+export declare function initWithRetry(deps: InitDeps): Promise<void>;
+//# sourceMappingURL=init.d.ts.map

package/dist/init.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../src/init.ts"],"names":[],"mappings":"AAEA,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,OAAO,GAAG,GAAG,IAAI,KAAK,GAAG;IAAE,IAAI,CAAC,EAAE,MAAM,CAAA;CAAE,CAElF;AAED,MAAM,WAAW,QAAQ;IACvB,MAAM,EAAE;QAAE,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC;QAAC,IAAI,IAAI,MAAM,CAAA;KAAE,CAAC;IAClD,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,OAAO,CAAC;IACjB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,EAAE,OAAO,EAAE,KAAK,IAAI,CAAC;CACpC;AAED,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,KAAK,GAAG;IAAE,IAAI,CAAC,EAAE,MAAM,CAAA;CAAE,EAAE,SAAS,EAAE,MAAM,GAAG,MAAM,CAS7F;AAED;;;GAGG;AACH,wBAAsB,aAAa,CAAC,IAAI,EAAE,QAAQ,GAAG,OAAO,CAAC,IAAI,CAAC,CA0BjE"}

package/dist/init.js

@@ -0,0 +1,46 @@
+import { StoreCorruptError } from '@nacho-labs/nachos-embeddings';
+export function isStoreCorruptError(err) {
+    return err instanceof StoreCorruptError || (err instanceof Error && err.name === 'StoreCorruptError');
+}
+export function corruptStoreMessage(err, storePath) {
+    const file = err.path ?? storePath;
+    return [
+        `[Init] The semantic store file is corrupt and could not be loaded: ${file}`,
+        `       ${err.message}`,
+        '       To fix it, do one of:',
+        '         - repair the file by hand, or delete it (the index will start empty)',
+        '         - set MCP_SEMANTIC_ON_CORRUPT_STORE=quarantine to rename the corrupt file aside and start empty',
+    ].join('\n');
+}
+/**
+ * Initialise the search index. Corrupt stores are never retried. Throws on final failure
+ * after logging an actionable message.
+ */
+export async function initWithRetry(deps) {
+    const { search, storePath, verbose, maxRetries = 3, retryDelayMs = 2000, log = console.error } = deps;
+    for (let attempt = 1; attempt <= maxRetries; attempt++) {
+        try {
+            if (verbose)
+                log(`[Init] Attempt ${attempt}/${maxRetries}`);
+            await search.init();
+            if (verbose)
+                log(`[Init] Loaded ${search.size()} documents`);
+            return;
+        }
+        catch (err) {
+            if (isStoreCorruptError(err)) {
+                log(corruptStoreMessage(err, storePath));
+                throw err;
+            }
+            if (attempt === maxRetries) {
+                log(`[Init] Failed after ${maxRetries} attempts: ${err instanceof Error ? err.message : String(err)}\n` +
+                    '       Check the store path, model name, and provider settings. If this is the first run, ' +
+                    'the model download (~25MB) needs network access, which is one possible cause.', err);
+                throw err;
+            }
+            log('[Init] Retry in 2s...', err);
+            await new Promise((r) => setTimeout(r, retryDelayMs));
+        }
+    }
+}
+//# sourceMappingURL=init.js.map

package/dist/init.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"init.js","sourceRoot":"","sources":["../src/init.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAE,MAAM,+BAA+B,CAAC;AAElE,MAAM,UAAU,mBAAmB,CAAC,GAAY;IAC9C,OAAO,GAAG,YAAY,iBAAiB,IAAI,CAAC,GAAG,YAAY,KAAK,IAAI,GAAG,CAAC,IAAI,KAAK,mBAAmB,CAAC,CAAC;AACxG,CAAC;AAWD,MAAM,UAAU,mBAAmB,CAAC,GAA8B,EAAE,SAAiB;IACnF,MAAM,IAAI,GAAG,GAAG,CAAC,IAAI,IAAI,SAAS,CAAC;IACnC,OAAO;QACL,sEAAsE,IAAI,EAAE;QAC5E,UAAU,GAAG,CAAC,OAAO,EAAE;QACvB,8BAA8B;QAC9B,+EAA+E;QAC/E,0GAA0G;KAC3G,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;AACf,CAAC;AAED;;;GAGG;AACH,MAAM,CAAC,KAAK,UAAU,aAAa,CAAC,IAAc;IAChD,MAAM,EAAE,MAAM,EAAE,SAAS,EAAE,OAAO,EAAE,UAAU,GAAG,CAAC,EAAE,YAAY,GAAG,IAAI,EAAE,GAAG,GAAG,OAAO,CAAC,KAAK,EAAE,GAAG,IAAI,CAAC;IACtG,KAAK,IAAI,OAAO,GAAG,CAAC,EAAE,OAAO,IAAI,UAAU,EAAE,OAAO,EAAE,EAAE,CAAC;QACvD,IAAI,CAAC;YACH,IAAI,OAAO;gBAAE,GAAG,CAAC,kBAAkB,OAAO,IAAI,UAAU,EAAE,CAAC,CAAC;YAC5D,MAAM,MAAM,CAAC,IAAI,EAAE,CAAC;YACpB,IAAI,OAAO;gBAAE,GAAG,CAAC,iBAAiB,MAAM,CAAC,IAAI,EAAE,YAAY,CAAC,CAAC;YAC7D,OAAO;QACT,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,IAAI,mBAAmB,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC7B,GAAG,CAAC,mBAAmB,CAAC,GAAG,EAAE,SAAS,CAAC,CAAC,CAAC;gBACzC,MAAM,GAAG,CAAC;YACZ,CAAC;YACD,IAAI,OAAO,KAAK,UAAU,EAAE,CAAC;gBAC3B,GAAG,CACD,uBAAuB,UAAU,cAAc,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI;oBACjG,4FAA4F;oBAC5F,+EAA+E,EACjF,GAAG,CACJ,CAAC;gBACF,MAAM,GAAG,CAAC;YACZ,CAAC;YACD,GAAG,CAAC,uBAAuB,EAAE,GAAG,CAAC,CAAC;YAClC,MAAM,IAAI,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,UAAU,CAAC,CAAC,EAAE,YAAY,CAAC,CAAC,CAAC;QACxD,CAAC;IACH,CAAC;AACH,CAAC"}

package/dist/op-queue.d.ts

@@ -0,0 +1,7 @@
+export declare class OpQueue {
+    private onError?;
+    private queue;
+    constructor(onError?: ((err: unknown) => void) | undefined);
+    run<T>(fn: () => Promise<T>): Promise<T>;
+}
+//# sourceMappingURL=op-queue.d.ts.map

package/dist/op-queue.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"op-queue.d.ts","sourceRoot":"","sources":["../src/op-queue.ts"],"names":[],"mappings":"AAAA,qBAAa,OAAO;IAGN,OAAO,CAAC,OAAO,CAAC;IAF5B,OAAO,CAAC,KAAK,CAAqB;IAElC,YAAoB,OAAO,CAAC,GAAE,CAAC,GAAG,EAAE,OAAO,KAAK,IAAI,aAAA,EAAI;IAElD,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,MAAM,OAAO,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,CAoB7C;CACF"}

package/dist/op-queue.js

@@ -0,0 +1,29 @@
+export class OpQueue {
+    onError;
+    queue = Promise.resolve();
+    constructor(onError) {
+        this.onError = onError;
+    }
+    async run(fn) {
+        const prev = this.queue;
+        let resolve;
+        this.queue = new Promise((res) => {
+            resolve = res;
+        });
+        try {
+            await prev.catch(() => { });
+            const result = await fn();
+            return result;
+        }
+        catch (err) {
+            if (this.onError) {
+                this.onError(err);
+            }
+            throw err;
+        }
+        finally {
+            resolve();
+        }
+    }
+}
+//# sourceMappingURL=op-queue.js.map

package/dist/op-queue.js.map

@@ -0,0 +1 @@
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package/dist/product.d.ts

@@ -0,0 +1,10 @@
+export declare const RESOURCE_URI_SCHEME = "semantic-search";
+export declare const RESOURCE_URI_HOST = "indexes";
+export declare const DEFAULT_INDEX_ID = "default";
+export declare function buildIndexBaseUri(indexId?: string): string;
+export declare function buildDocumentResourceUri(documentId: string, indexId?: string): string;
+export declare const INDEX_MANIFEST_URI: string;
+export declare const INDEX_STATS_URI: string;
+export declare const DOCUMENT_RESOURCE_TEMPLATE_URI = "semantic-search://indexes/{indexId}/documents/{documentId}";
+export declare const REGISTERED_RESOURCE_URIS: readonly [string, string];
+//# sourceMappingURL=product.d.ts.map

package/dist/product.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"product.d.ts","sourceRoot":"","sources":["../src/product.ts"],"names":[],"mappings":"AAAA,eAAO,MAAM,mBAAmB,oBAAoB,CAAC;AACrD,eAAO,MAAM,iBAAiB,YAAY,CAAC;AAC3C,eAAO,MAAM,gBAAgB,YAAY,CAAC;AAE1C,wBAAgB,iBAAiB,CAAC,OAAO,SAAmB,GAAG,MAAM,CAEpE;AAED,wBAAgB,wBAAwB,CAAC,UAAU,EAAE,MAAM,EAAE,OAAO,SAAmB,GAAG,MAAM,CAE/F;AAED,eAAO,MAAM,kBAAkB,QAAoC,CAAC;AACpE,eAAO,MAAM,eAAe,QAAiC,CAAC;AAC9D,eAAO,MAAM,8BAA8B,+DAAmF,CAAC;AAC/H,eAAO,MAAM,wBAAwB,2BAAiD,CAAC"}

package/dist/product.js

@@ -0,0 +1,14 @@
+export const RESOURCE_URI_SCHEME = 'semantic-search';
+export const RESOURCE_URI_HOST = 'indexes';
+export const DEFAULT_INDEX_ID = 'default';
+export function buildIndexBaseUri(indexId = DEFAULT_INDEX_ID) {
+    return `${RESOURCE_URI_SCHEME}://${RESOURCE_URI_HOST}/${encodeURIComponent(indexId)}`;
+}
+export function buildDocumentResourceUri(documentId, indexId = DEFAULT_INDEX_ID) {
+    return `${buildIndexBaseUri(indexId)}/documents/${encodeURIComponent(documentId)}`;
+}
+export const INDEX_MANIFEST_URI = `${buildIndexBaseUri()}/manifest`;
+export const INDEX_STATS_URI = `${buildIndexBaseUri()}/stats`;
+export const DOCUMENT_RESOURCE_TEMPLATE_URI = `${RESOURCE_URI_SCHEME}://${RESOURCE_URI_HOST}/{indexId}/documents/{documentId}`;
+export const REGISTERED_RESOURCE_URIS = [INDEX_MANIFEST_URI, INDEX_STATS_URI];
+//# sourceMappingURL=product.js.map

package/dist/product.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"product.js","sourceRoot":"","sources":["../src/product.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,mBAAmB,GAAG,iBAAiB,CAAC;AACrD,MAAM,CAAC,MAAM,iBAAiB,GAAG,SAAS,CAAC;AAC3C,MAAM,CAAC,MAAM,gBAAgB,GAAG,SAAS,CAAC;AAE1C,MAAM,UAAU,iBAAiB,CAAC,OAAO,GAAG,gBAAgB;IAC1D,OAAO,GAAG,mBAAmB,MAAM,iBAAiB,IAAI,kBAAkB,CAAC,OAAO,CAAC,EAAE,CAAC;AACxF,CAAC;AAED,MAAM,UAAU,wBAAwB,CAAC,UAAkB,EAAE,OAAO,GAAG,gBAAgB;IACrF,OAAO,GAAG,iBAAiB,CAAC,OAAO,CAAC,cAAc,kBAAkB,CAAC,UAAU,CAAC,EAAE,CAAC;AACrF,CAAC;AAED,MAAM,CAAC,MAAM,kBAAkB,GAAG,GAAG,iBAAiB,EAAE,WAAW,CAAC;AACpE,MAAM,CAAC,MAAM,eAAe,GAAG,GAAG,iBAAiB,EAAE,QAAQ,CAAC;AAC9D,MAAM,CAAC,MAAM,8BAA8B,GAAG,GAAG,mBAAmB,MAAM,iBAAiB,mCAAmC,CAAC;AAC/H,MAAM,CAAC,MAAM,wBAAwB,GAAG,CAAC,kBAAkB,EAAE,eAAe,CAAU,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@nacho-labs/mcp-semantic-search",
-  "version": "0.3.3",
+  "version": "0.5.0",
   "description": "MCP server for semantic search — give Claude Code, Cursor, and other AI tools persistent memory via local Transformers.js or AWS Bedrock embeddings",
   "type": "module",
   "main": "./dist/index.js",
@@ -28,8 +28,8 @@
     "lint": "eslint .",
     "format": "prettier --write .",
     "format:check": "prettier --check .",
-    "test:unit": "node --test test/integration-support.test.mjs test/release-contract.test.mjs",
-    "test:integration": "npm run build && node --test test/stdio-smoke.test.mjs",
+    "test:unit": "npm run build && node --test test/integration-support.test.mjs test/release-contract.test.mjs test/op-queue.test.mjs test/config-init.test.mjs",
+    "test:integration": "npm run build && node --test test/stdio-smoke.test.mjs test/corrupt-store.test.mjs",
     "test": "npm run test:unit",
     "clean": "rm -rf dist *.tsbuildinfo",
     "prepublishOnly": "npm run build",
@@ -65,25 +65,24 @@
     "url": "git+https://github.com/Nacho-Labs-LLC/mcp-semantic-search.git"
   },
   "dependencies": {
-    "@modelcontextprotocol/sdk": "^1.30.0",
-    "@nacho-labs/nachos-embeddings": "^0.5.1",
-    "zod": "^4.4.3"
+    "@modelcontextprotocol/sdk": "^1.32.2",
+    "@nacho-labs/nachos-embeddings": "^0.6.0",
+    "zod": "^4.6.7"
   },
   "optionalDependencies": {
-    "@aws-sdk/client-bedrock-runtime": "^3.1101.0"
+    "@aws-sdk/client-bedrock-runtime": "^3.1161.0"
   },
   "overrides": {
-    "adm-zip": "0.6.0",
-    "sharp": "0.35.3"
+    "adm-zip": "0.6.1",
+    "sharp": "0.35.5"
   },
   "devDependencies": {
-    "@aws-sdk/client-bedrock-runtime": "^3.1101.0",
-    "@babel/core": "^7.29.7",
-    "@babel/eslint-parser": "^7.29.7",
-    "@babel/preset-typescript": "^7.29.7",
-    "@eslint/js": "^9.39.5",
-    "@types/node": "^26.1.2",
-    "eslint": "^9.39.5",
+    "@aws-sdk/client-bedrock-runtime": "^3.1161.0",
+    "@babel/core": "^8.0.10",
+    "@babel/eslint-parser": "^8.0.1",
+    "@eslint/js": "^10.0.1",
+    "@types/node": "^26.6.6",
+    "eslint": "^10.14.0",
     "prettier": "^3.9.6",
     "typescript": "^7.0.2"
   }

package/server.json

@@ -3,7 +3,7 @@
   "name": "io.github.nacho-labs-llc/mcp-semantic-search",
   "description": "Local semantic search for AI coding tools. Index decisions, patterns, and context — recall them by meaning, not keywords. Powered by nachos-embeddings (Transformers.js). No API keys, no cloud, no costs.",
   "title": "Semantic Search MCP Server",
-  "version": "0.3.2",
+  "version": "0.5.0",
   "repository": {
     "url": "https://github.com/nacho-labs-llc/mcp-semantic-search",
     "source": "github"
@@ -12,7 +12,7 @@
     {
       "registryType": "npm",
       "identifier": "@nacho-labs/mcp-semantic-search",
-      "version": "0.3.2",
+      "version": "0.5.0",
       "transport": {
         "type": "stdio"
       },
@@ -40,7 +40,14 @@
         },
         {
           "name": "MCP_SEMANTIC_CACHE_DIR",
-          "description": "Model cache directory. Defaults to .cache/transformers.",
+          "description": "Model cache directory. Defaults to the nachos-embeddings per-user cache ($NACHOS_EMBEDDINGS_CACHE, else XDG, else ~/.cache/nachos-embeddings).",
+          "isRequired": false,
+          "isSecret": false,
+          "format": "string"
+        },
+        {
+          "name": "MCP_SEMANTIC_ON_CORRUPT_STORE",
+          "description": "What to do when the store file is corrupt: throw (exit with an error) or quarantine (rename the file aside and start empty). Defaults to throw.",
           "isRequired": false,
           "isSecret": false,
           "format": "string"