kibi-cli 0.2.7 → 0.3.0

package/dist/commands/doctor.js

@@ -198,7 +198,7 @@ function checkGitHooks() {
     return {
         passed: false,
         message: "Partially installed",
-        remediation: "Run: kibi init --hooks",
+        remediation: "Run: kibi init",
     };
 }
 function checkPreCommitHook() {
@@ -218,7 +218,7 @@ function checkPreCommitHook() {
         return {
             passed: false,
             message: "Not installed",
-            remediation: "Run: kibi init --hooks",
+            remediation: "Run: kibi init",
         };
     }
     try {
@@ -233,7 +233,7 @@ function checkPreCommitHook() {
             return {
                 passed: false,
                 message: "pre-commit hook installed but does not invoke kibi",
-                remediation: "Run: kibi init --hooks to install recommended hooks",
+                remediation: "Run: kibi init to install recommended hooks",
             };
         }
         if (preCommitExecutable) {
@@ -247,7 +247,7 @@ function checkPreCommitHook() {
             return {
                 passed: true,
                 message: "Installed and executable (uses legacy 'kibi check' — consider running 'kibi init' to update hooks to use '--staged')",
-                remediation: "Run: kibi init --hooks to update git hooks to the latest template",
+                remediation: "Run: kibi init to update git hooks to the latest template",
             };
         }
         return {
@@ -260,7 +260,7 @@ function checkPreCommitHook() {
         return {
             passed: false,
             message: "Unable to check hook permissions or read content",
-            remediation: "Run: kibi init --hooks",
+            remediation: "Run: kibi init",
         };
     }
 }
@@ -281,7 +281,7 @@ function checkPostRewriteHook() {
         return {
             passed: false,
             message: "Not installed",
-            remediation: "Run: kibi init --hooks",
+            remediation: "Run: kibi init",
         };
     }
     try {
@@ -294,7 +294,7 @@ function checkPostRewriteHook() {
             return {
                 passed: false,
                 message: "post-rewrite hook installed but does not invoke kibi",
-                remediation: "Run: kibi init --hooks to install recommended hooks",
+                remediation: "Run: kibi init to install recommended hooks",
             };
         }
         if (postRewriteExecutable) {
@@ -313,7 +313,7 @@ function checkPostRewriteHook() {
         return {
             passed: false,
             message: "Unable to check hook permissions or read content",
-            remediation: "Run: kibi init --hooks",
+            remediation: "Run: kibi init",
         };
     }
 }

package/dist/commands/gaps.d.ts

@@ -0,0 +1,12 @@
+interface GapsOptions {
+    missingRel?: string;
+    presentRel?: string;
+    tag?: string;
+    source?: string;
+    limit?: string;
+    offset?: string;
+    format?: "json" | "table";
+}
+export declare function gapsCommand(type: string | undefined, options: GapsOptions): Promise<void>;
+export {};
+//# sourceMappingURL=gaps.d.ts.map

package/dist/commands/gaps.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"gaps.d.ts","sourceRoot":"","sources":["../../src/commands/gaps.ts"],"names":[],"mappings":"AAQA,UAAU,WAAW;IACnB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,MAAM,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;CAC3B;AAGD,wBAAsB,WAAW,CAC/B,IAAI,EAAE,MAAM,GAAG,SAAS,EACxB,OAAO,EAAE,WAAW,GACnB,OAAO,CAAC,IAAI,CAAC,CAyBf"}

package/dist/commands/gaps.js

@@ -0,0 +1,28 @@
+import { escapeAtom } from "../prolog/codec.js";
+import { printDiscoveryResult, resolveCurrentKbPath, runJsonModuleQuery, withPrologProcess, } from "./discovery-shared.js";
+// implements REQ-002, REQ-003
+export async function gapsCommand(type, options) {
+    await withPrologProcess(async (prolog) => {
+        const kbPath = await resolveCurrentKbPath();
+        const missing = csvToPrologList(options.missingRel);
+        const present = csvToPrologList(options.presentRel);
+        const tags = csvToPrologList(options.tag);
+        const source = options.source ? `'${escapeAtom(options.source)}'` : "none";
+        const limit = Number.parseInt(options.limit || "100", 10);
+        const offset = Number.parseInt(options.offset || "0", 10);
+        const typeArg = type ? `'${escapeAtom(type)}'` : "none";
+        const result = await runJsonModuleQuery(prolog, "discovery.pl", `discovery:find_gaps_json(${typeArg}, ${missing}, ${present}, ${tags}, ${source}, ${limit}, ${offset}, JsonString)`, "gaps query failed", kbPath);
+        printDiscoveryResult(options.format, result, `Found ${result.count ?? 0} gap rows.`);
+    });
+}
+function csvToPrologList(value) {
+    if (!value?.trim()) {
+        return "[]";
+    }
+    return `[${value
+        .split(",")
+        .map((item) => item.trim())
+        .filter(Boolean)
+        .map((item) => `'${escapeAtom(item)}'`)
+        .join(",")}]`;
+}

package/dist/commands/graph.d.ts

@@ -0,0 +1,13 @@
+interface GraphOptions {
+    from?: string;
+    relationships?: string;
+    direction?: "outgoing" | "incoming" | "both";
+    depth?: string;
+    entityTypes?: string;
+    maxNodes?: string;
+    maxEdges?: string;
+    format?: "json" | "table";
+}
+export declare function graphCommand(options: GraphOptions): Promise<void>;
+export {};
+//# sourceMappingURL=graph.d.ts.map

package/dist/commands/graph.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"graph.d.ts","sourceRoot":"","sources":["../../src/commands/graph.ts"],"names":[],"mappings":"AAQA,UAAU,YAAY;IACpB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,SAAS,CAAC,EAAE,UAAU,GAAG,UAAU,GAAG,MAAM,CAAC;IAC7C,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;CAC3B;AAGD,wBAAsB,YAAY,CAAC,OAAO,EAAE,YAAY,GAAG,OAAO,CAAC,IAAI,CAAC,CAiCvE"}

package/dist/commands/graph.js

@@ -0,0 +1,35 @@
+import { escapeAtom } from "../prolog/codec.js";
+import { printDiscoveryResult, resolveCurrentKbPath, runJsonModuleQuery, withPrologProcess, } from "./discovery-shared.js";
+// implements REQ-002, REQ-003
+export async function graphCommand(options) {
+    if (!options.from?.trim()) {
+        console.error("Error: --from is required");
+        process.exitCode = 1;
+        return;
+    }
+    await withPrologProcess(async (prolog) => {
+        const kbPath = await resolveCurrentKbPath();
+        const seedIds = csvToPrologList(options.from);
+        const relationships = csvToPrologList(options.relationships);
+        const direction = options.direction || "outgoing";
+        const depth = Number.parseInt(options.depth || "1", 10);
+        const entityTypes = csvToPrologList(options.entityTypes);
+        const maxNodes = Number.parseInt(options.maxNodes || "200", 10);
+        const maxEdges = Number.parseInt(options.maxEdges || "500", 10);
+        const result = await runJsonModuleQuery(prolog, "discovery.pl", `discovery:graph_expand_json(${seedIds}, ${relationships}, '${direction}', ${depth}, ${entityTypes}, ${maxNodes}, ${maxEdges}, JsonString)`, "graph query failed", kbPath);
+        const nodes = Array.isArray(result.nodes) ? result.nodes.length : 0;
+        const edges = Array.isArray(result.edges) ? result.edges.length : 0;
+        printDiscoveryResult(options.format, result, `Graph traversal returned ${nodes} nodes and ${edges} edges.`);
+    });
+}
+function csvToPrologList(value) {
+    if (!value?.trim()) {
+        return "[]";
+    }
+    return `[${value
+        .split(",")
+        .map((item) => item.trim())
+        .filter(Boolean)
+        .map((item) => `'${escapeAtom(item)}'`)
+        .join(",")}]`;
+}

package/dist/commands/query.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"query.d.ts","sourceRoot":"","sources":["../../src/commands/query.ts"],"names":[],"mappings":"AA2CA,UAAU,YAAY;IACpB,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,MAAM,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IAC1B,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAGD,wBAAsB,YAAY,CAChC,IAAI,EAAE,MAAM,GAAG,SAAS,EACxB,OAAO,EAAE,YAAY,GACpB,OAAO,CAAC,IAAI,CAAC,CAgLf"}
+{"version":3,"file":"query.d.ts","sourceRoot":"","sources":["../../src/commands/query.ts"],"names":[],"mappings":"AA2CA,UAAU,YAAY;IACpB,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,MAAM,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IAC1B,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAGD,wBAAsB,YAAY,CAChC,IAAI,EAAE,MAAM,GAAG,SAAS,EACxB,OAAO,EAAE,YAAY,GACpB,OAAO,CAAC,IAAI,CAAC,CAyKf"}

package/dist/commands/query.js

@@ -31,7 +31,6 @@ export async function queryCommand(type, options) {
         prolog = new PrologProcess({ timeout: 120000 });
         await prolog.start();
         await prolog.query("set_prolog_flag(answer_write_options, [max_depth(0), spacing(next_argument)])");
-        // Resolve branch: allow non-git repos to use default "main" for query
         let currentBranch;
         const branchResult = resolveActiveBranch();
         if ("error" in branchResult) {
@@ -61,12 +60,11 @@ export async function queryCommand(type, options) {
         }
         attached = true;
         let results = [];
-        // Query relationships mode
         if (options.relationships) {
             const fromId = String(options.relationships);
             const safeFromId = fromId.replace(/'/g, "''");
-            // Query all relationship types for the given source ID
-            const goal = `findall([Type,From,To], (From='${safeFromId}', kb_relationship(Type, From, To)), Results)`;
+            const relTypesList = REL_TYPES.join(", ");
+            const goal = `findall([Type,From,To], (member(Type, [${relTypesList}]), kb_relationship(Type, '${safeFromId}', To), From='${safeFromId}'), Results)`;
             const queryResult = await prolog.query(goal);
             if (queryResult.success && queryResult.bindings.Results) {
                 const rows = parseListOfLists(queryResult.bindings.Results);
@@ -85,9 +83,7 @@ export async function queryCommand(type, options) {
                     REL_TYPES.includes(rel.type));
             }
         }
-        // Query entities mode
         else if (type || options.source) {
-            // Validate type if provided
             if (type && !VALID_ENTITY_TYPES.includes(type)) {
                 console.error(`Error: Invalid type '${type}'. Valid types: ${VALID_ENTITY_TYPES.join(", ")}`);
                 process.exitCode = 1;
@@ -95,7 +91,6 @@ export async function queryCommand(type, options) {
             }
             let goal;
             if (options.source) {
-                // Query by source path (substring match)
                 const safeSource = String(options.source).replace(/'/g, "\\'");
                 if (type) {
                     goal = `findall([Id,'${type}',Props], (kb_entities_by_source('${safeSource}', SourceIds), member(Id, SourceIds), kb_entity(Id, '${type}', Props)), Results)`;
@@ -141,7 +136,6 @@ export async function queryCommand(type, options) {
             process.exitCode = 1;
             return;
         }
-        // Apply pagination
         const limit = Number.parseInt(options.limit || "100");
         const offset = Number.parseInt(options.offset || "0");
         const paginated = results.slice(offset, offset + limit);

package/dist/commands/search.d.ts

@@ -0,0 +1,9 @@
+interface SearchOptions {
+    type?: string;
+    format?: "json" | "table";
+    limit?: string;
+    offset?: string;
+}
+export declare function searchCommand(query: string | undefined, options: SearchOptions): Promise<void>;
+export {};
+//# sourceMappingURL=search.d.ts.map

package/dist/commands/search.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"search.d.ts","sourceRoot":"","sources":["../../src/commands/search.ts"],"names":[],"mappings":"AAYA,UAAU,aAAa;IACrB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,MAAM,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IAC1B,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAGD,wBAAsB,aAAa,CACjC,KAAK,EAAE,MAAM,GAAG,SAAS,EACzB,OAAO,EAAE,aAAa,GACrB,OAAO,CAAC,IAAI,CAAC,CAqBf"}

package/dist/commands/search.js

@@ -0,0 +1,38 @@
+import { rankEntities } from "../search-ranking.js";
+import { VALID_ENTITY_TYPES, queryEntities, } from "../query/service.js";
+import { printDiscoveryResult, withAttachedBranchProlog, } from "./discovery-shared.js";
+// implements REQ-mcp-search-discovery, REQ-003
+export async function searchCommand(query, options) {
+    if (!query?.trim()) {
+        console.error("Error: search query is required");
+        process.exitCode = 1;
+        return;
+    }
+    if (options.type && !VALID_ENTITY_TYPES.includes(options.type)) {
+        console.error(`Error: invalid type '${options.type}'. Valid types: ${VALID_ENTITY_TYPES.join(", ")}`);
+        process.exitCode = 1;
+        return;
+    }
+    await withAttachedBranchProlog(async (prolog) => {
+        const limit = Number.parseInt(options.limit || "20", 10);
+        const offset = Number.parseInt(options.offset || "0", 10);
+        const result = await executeSearch(prolog, query, options.type, limit, offset);
+        printDiscoveryResult(options.format, result, buildSearchText(query, result));
+    });
+}
+async function executeSearch(prolog, query, type, limit, offset) {
+    const entitiesResult = await queryEntities(prolog, {
+        type,
+        limit: 100000,
+        offset: 0,
+    });
+    const matches = await rankEntities(entitiesResult.entities, query, process.cwd());
+    const paginated = matches.slice(offset, offset + limit);
+    return { results: paginated, count: matches.length };
+}
+function buildSearchText(query, result) {
+    if (result.count === 0) {
+        return `No search results for '${query}'.`;
+    }
+    return `Found ${result.count} search results for '${query}'. Showing ${result.results.length}: ${result.results.map((match) => match.entity.id).join(", ")}`;
+}

package/dist/commands/status.d.ts

@@ -0,0 +1,6 @@
+interface StatusOptions {
+    format?: "json" | "table";
+}
+export declare function statusCommand(options: StatusOptions): Promise<void>;
+export {};
+//# sourceMappingURL=status.d.ts.map

package/dist/commands/status.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"status.d.ts","sourceRoot":"","sources":["../../src/commands/status.ts"],"names":[],"mappings":"AAOA,UAAU,aAAa;IACrB,MAAM,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;CAC3B;AAGD,wBAAsB,aAAa,CAAC,OAAO,EAAE,aAAa,GAAG,OAAO,CAAC,IAAI,CAAC,CAgBzE"}

package/dist/commands/status.js

@@ -0,0 +1,9 @@
+import { printDiscoveryResult, resolveCurrentKbPath, runJsonModuleQuery, withPrologProcess, } from "./discovery-shared.js";
+// implements REQ-002, REQ-003
+export async function statusCommand(options) {
+    await withPrologProcess(async (prolog) => {
+        const kbPath = await resolveCurrentKbPath();
+        const result = await runJsonModuleQuery(prolog, "status.pl", "status:kb_status_json(JsonString)", "status query failed", kbPath);
+        printDiscoveryResult(options.format, result, `Branch ${result.branch} is ${result.syncState} (dirty=${result.dirty})`);
+    });
+}

package/dist/commands/sync.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"sync.d.ts","sourceRoot":"","sources":["../../src/commands/sync.ts"],"names":[],"mappings":"AAqBA,OAAO,KAAK,EAAc,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAyCjE,qBAAa,SAAU,SAAQ,KAAK;gBACtB,OAAO,EAAE,MAAM;CAI5B;AAGD,wBAAsB,WAAW,CAC/B,OAAO,GAAE;IACP,YAAY,CAAC,EAAE,OAAO,CAAC;IACvB,OAAO,CAAC,EAAE,OAAO,CAAC;CACd,GACL,OAAO,CAAC,WAAW,CAAC,CA0WtB;AAGD,OAAO,EAAE,qBAAqB,EAAE,MAAM,qBAAqB,CAAC"}
+{"version":3,"file":"sync.d.ts","sourceRoot":"","sources":["../../src/commands/sync.ts"],"names":[],"mappings":"AAqBA,OAAO,KAAK,EAAc,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAyCjE,qBAAa,SAAU,SAAQ,KAAK;gBACtB,OAAO,EAAE,MAAM;CAI5B;AAGD,wBAAsB,WAAW,CAC/B,OAAO,GAAE;IACP,YAAY,CAAC,EAAE,OAAO,CAAC;IACvB,OAAO,CAAC,EAAE,OAAO,CAAC;CACd,GACL,OAAO,CAAC,WAAW,CAAC,CA4VtB;AAED,OAAO,EAAE,qBAAqB,EAAE,MAAM,qBAAqB,CAAC"}

package/dist/commands/sync.js

@@ -74,10 +74,8 @@ export async function syncCommand(options = {}) {
             }
             catch { }
         }
-        // Load config
         const config = loadSyncConfig(process.cwd());
         const paths = config.paths;
-        // File discovery
         const { markdownFiles, manifestFiles, relationshipsDir } = await discoverSourceFiles(process.cwd(), paths);
         if (process.env.KIBI_DEBUG) {
             try {
@@ -95,12 +93,10 @@ export async function syncCommand(options = {}) {
         const nowMs = Date.now();
         const nextHashes = {};
         const nextSeenAt = {};
-        // Extract relationships from shard files
         const shardResults = extractFromRelationshipShards(relationshipsDir);
         const allRelationships = flattenRelationships(shardResults);
         const changedMarkdownFiles = [];
         const changedManifestFiles = [];
-        // Detect changed files
         for (const file of sourceFiles) {
             try {
                 const key = toCacheKey(file);
@@ -129,7 +125,6 @@ export async function syncCommand(options = {}) {
         }
         const performedFullReindex = changedMarkdownFiles.length === markdownFiles.length &&
             changedManifestFiles.length === manifestFiles.length;
-        // Content extraction
         const { results, failedCacheKeys, errors } = await processExtractions(changedMarkdownFiles, changedManifestFiles, validateOnly);
         // Collect INVALID_AUTHORING diagnostics
         for (const err of errors) {
@@ -160,7 +155,6 @@ export async function syncCommand(options = {}) {
                 process.exit(0);
             }
         }
-        // Refresh symbol manifest coordinates
         for (const file of manifestFiles) {
             try {
                 await refreshManifestCoordinates(file, process.cwd());
@@ -170,7 +164,6 @@ export async function syncCommand(options = {}) {
                 console.warn(`Warning: Failed to refresh symbol coordinates in ${file}: ${message}`);
             }
         }
-        // Early exit if no changes
         if (results.length === 0 && allRelationships.length === 0 && !rebuild) {
             const evictedHashes = {};
             const evictedSeenAt = {};
@@ -189,7 +182,6 @@ export async function syncCommand(options = {}) {
             console.log("✓ Imported 0 entities, 0 relationships (no changes)");
             process.exit(0);
         }
-        // Staging setup
         const livePath = path.join(process.cwd(), `.kb/branches/${currentBranch}`);
         const kbExists = existsSync(livePath);
         if (!kbExists && !rebuild) {
@@ -197,7 +189,6 @@ export async function syncCommand(options = {}) {
         }
         const stagingPath = path.join(process.cwd(), `.kb/branches/${currentBranch}.staging`);
         await prepareStagingEnvironment(stagingPath, livePath, rebuild);
-        // Persistence to KB
         try {
             const prolog = new PrologProcess({ timeout: 120000 });
             await prolog.start();
@@ -207,13 +198,10 @@ export async function syncCommand(options = {}) {
                 throw new SyncError(`Failed to attach to staging KB: ${attachResult.error || "Unknown error"}`);
             }
             const entityIds = new Set();
-            // Track entity counts by type
             for (const { entity } of results) {
                 entityCounts[entity.type] = (entityCounts[entity.type] || 0) + 1;
             }
-            // Persist entities
             const { entityCount, kbModified: entitiesModified } = await persistEntities(prolog, results, entityIds);
-            // Validate and filter dangling relationships after entity IDs are known.
             const validationErrors = validateRelationships(allRelationships, entityIds);
             if (validationErrors.length > 0) {
                 console.warn(`Warning: ${validationErrors.length} dangling relationship(s) found`);
@@ -235,9 +223,7 @@ export async function syncCommand(options = {}) {
             }
             await prolog.query("kb_detach");
             await prolog.terminate();
-            // Publish staging to live
             atomicPublish(stagingPath, livePath);
-            // Update cache
             const evictedHashes = {};
             const evictedSeenAt = {};
             for (const [key, hash] of Object.entries(nextHashes)) {
@@ -304,5 +290,4 @@ export async function syncCommand(options = {}) {
         throw error;
     }
 }
-// Export for use by modules that need these functions
 export { normalizeMarkdownPath } from "./sync/discovery.js";

package/dist/diagnostics.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"diagnostics.d.ts","sourceRoot":"","sources":["../src/diagnostics.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,MAAM,MAAM,kBAAkB,GAC1B,2BAA2B,GAC3B,YAAY,GACZ,kBAAkB,GAClB,mBAAmB,GACnB,YAAY,GACZ,kBAAkB,GAClB,oBAAoB,CAAC;AAEzB,MAAM,WAAW,UAAU;IACzB,QAAQ,EAAE,kBAAkB,CAAC;IAC7B,QAAQ,EAAE,OAAO,GAAG,SAAS,CAAC;IAC9B,OAAO,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,WAAW,WAAW;IAC1B,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACrC,iBAAiB,EAAE,MAAM,CAAC;IAC1B,OAAO,EAAE,OAAO,CAAC;IACjB,SAAS,EAAE,OAAO,CAAC;IACnB,QAAQ,EAAE,UAAU,EAAE,CAAC;IACvB,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED;;GAEG;AACH,MAAM,MAAM,eAAe,GACvB,eAAe,GACf,eAAe,GACf,mBAAmB,GACnB,gBAAgB,GAChB,cAAc,GACd,eAAe,CAAC;AAEpB;;GAEG;AACH,wBAAgB,uBAAuB,CACrC,IAAI,EAAE,eAAe,EACrB,OAAO,EAAE,MAAM,EACf,MAAM,CAAC,EAAE,MAAM,GACd,UAAU,CASZ;AAED;;GAEG;AACH,wBAAgB,yBAAyB,CACvC,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,MAAM,GACX,UAAU,CAOZ;AAED;;GAEG;AACH,wBAAgB,8BAA8B,CAC5C,QAAQ,EAAE,MAAM,EAChB,WAAW,EAAE,MAAM,GAClB,UAAU,CAQZ;AAED;;GAEG;AACH,wBAAgB,gCAAgC,CAC9C,QAAQ,EAAE,MAAM,EAChB,aAAa,EAAE,MAAM,EAAE,GACtB,UAAU,CAQZ;AAED;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,OAAO,EAAE,WAAW,GAAG,MAAM,CAmD9D;AAED;;GAEG;AACH,wBAAgB,uBAAuB,CACrC,WAAW,EAAE,UAAU,EAAE,GACxB,KAAK,CAAC;IACP,QAAQ,EAAE,MAAM,CAAC;IACjB,QAAQ,EAAE,MAAM,CAAC;IACjB,OAAO,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB,CAAC,CAQD"}
+{"version":3,"file":"diagnostics.d.ts","sourceRoot":"","sources":["../src/diagnostics.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,MAAM,MAAM,kBAAkB,GAC1B,2BAA2B,GAC3B,YAAY,GACZ,kBAAkB,GAClB,mBAAmB,GACnB,YAAY,GACZ,kBAAkB,GAClB,oBAAoB,CAAC;AAEzB,MAAM,WAAW,UAAU;IACzB,QAAQ,EAAE,kBAAkB,CAAC;IAC7B,QAAQ,EAAE,OAAO,GAAG,SAAS,CAAC;IAC9B,OAAO,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,WAAW,WAAW;IAC1B,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACrC,iBAAiB,EAAE,MAAM,CAAC;IAC1B,OAAO,EAAE,OAAO,CAAC;IACjB,SAAS,EAAE,OAAO,CAAC;IACnB,QAAQ,EAAE,UAAU,EAAE,CAAC;IACvB,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED;;GAEG;AACH,MAAM,MAAM,eAAe,GACvB,eAAe,GACf,eAAe,GACf,mBAAmB,GACnB,gBAAgB,GAChB,cAAc,GACd,eAAe,CAAC;AAEpB;;GAEG;AACH,wBAAgB,uBAAuB,CACrC,IAAI,EAAE,eAAe,EACrB,OAAO,EAAE,MAAM,EACf,MAAM,CAAC,EAAE,MAAM,GACd,UAAU,CASZ;AAED;;GAEG;AACH,wBAAgB,yBAAyB,CACvC,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,MAAM,GACX,UAAU,CAOZ;AAED;;GAEG;AACH,wBAAgB,8BAA8B,CAC5C,QAAQ,EAAE,MAAM,EAChB,WAAW,EAAE,MAAM,GAClB,UAAU,CAQZ;AAED;;GAEG;AACH,wBAAgB,gCAAgC,CAC9C,QAAQ,EAAE,MAAM,EAChB,aAAa,EAAE,MAAM,EAAE,GACtB,UAAU,CAQZ;AAED;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,OAAO,EAAE,WAAW,GAAG,MAAM,CAiD9D;AAED;;GAEG;AACH,wBAAgB,uBAAuB,CAAC,WAAW,EAAE,UAAU,EAAE,GAAG,KAAK,CAAC;IACxE,QAAQ,EAAE,MAAM,CAAC;IACjB,QAAQ,EAAE,MAAM,CAAC;IACjB,OAAO,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB,CAAC,CAQD"}

package/dist/diagnostics.js

@@ -77,13 +77,11 @@ export function formatSyncSummary(summary) {
     }
     lines.push(`Total Relationships: ${summary.relationshipCount}`);
     lines.push("");
-    // Status
     lines.push(`Status: ${summary.success ? "✓ Success" : "✗ Failed"}`);
     lines.push(`Published: ${summary.published ? "Yes" : "No"}`);
     if (summary.durationMs !== undefined) {
         lines.push(`Duration: ${summary.durationMs}ms`);
     }
-    // Failures
     if (summary.failures.length > 0) {
         lines.push("");
         lines.push(`Failures (${summary.failures.length}):`);

package/dist/extractors/manifest.d.ts

@@ -20,6 +20,8 @@ export interface ExtractedRelationship {
 export interface ExtractionResult {
     entity: ExtractedEntity;
     relationships: ExtractedRelationship[];
+    /** The per-symbol source code file, distinct from the manifest file path. */
+    sourceFile?: string;
 }
 export declare class ManifestError extends Error {
     filePath: string;

package/dist/extractors/manifest.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"manifest.d.ts","sourceRoot":"","sources":["../../src/extractors/manifest.ts"],"names":[],"mappings":"AAsBA,MAAM,WAAW,eAAe;IAC9B,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,MAAM,CAAC;IACf,UAAU,EAAE,MAAM,CAAC;IACnB,UAAU,EAAE,MAAM,CAAC;IACnB,MAAM,EAAE,MAAM,CAAC;IACf,IAAI,CAAC,EAAE,MAAM,EAAE,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,qBAAqB;IACpC,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,EAAE,EAAE,MAAM,CAAC;CACZ;AAED,MAAM,WAAW,gBAAgB;IAC/B,MAAM,EAAE,eAAe,CAAC;IACxB,aAAa,EAAE,qBAAqB,EAAE,CAAC;CACxC;AAED,qBAAa,aAAc,SAAQ,KAAK;IAG7B,QAAQ,EAAE,MAAM;gBADvB,OAAO,EAAE,MAAM,EACR,QAAQ,EAAE,MAAM;CAK1B;AAuBD,wBAAgB,mBAAmB,CAAC,QAAQ,EAAE,MAAM,GAAG,gBAAgB,EAAE,CA4FxE"}
+{"version":3,"file":"manifest.d.ts","sourceRoot":"","sources":["../../src/extractors/manifest.ts"],"names":[],"mappings":"AAsBA,MAAM,WAAW,eAAe;IAC9B,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,MAAM,CAAC;IACf,UAAU,EAAE,MAAM,CAAC;IACnB,UAAU,EAAE,MAAM,CAAC;IACnB,MAAM,EAAE,MAAM,CAAC;IACf,IAAI,CAAC,EAAE,MAAM,EAAE,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,qBAAqB;IACpC,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,EAAE,EAAE,MAAM,CAAC;CACZ;AAED,MAAM,WAAW,gBAAgB;IAC/B,MAAM,EAAE,eAAe,CAAC;IACxB,aAAa,EAAE,qBAAqB,EAAE,CAAC;IACvC,6EAA6E;IAC7E,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED,qBAAa,aAAc,SAAQ,KAAK;IAG7B,QAAQ,EAAE,MAAM;gBADvB,OAAO,EAAE,MAAM,EACR,QAAQ,EAAE,MAAM;CAK1B;AAwBD,wBAAgB,mBAAmB,CAAC,QAAQ,EAAE,MAAM,GAAG,gBAAgB,EAAE,CA6FxE"}

package/dist/extractors/manifest.js

@@ -94,6 +94,7 @@ export function extractFromManifest(filePath) {
                     text_ref: symbol.text_ref,
                 },
                 relationships,
+                sourceFile: symbol.sourceFile ?? symbol.source,
             };
         });
     }

package/dist/extractors/markdown.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"markdown.d.ts","sourceRoot":"","sources":["../../src/extractors/markdown.ts"],"names":[],"mappings":"AAsBA,MAAM,WAAW,eAAe;IAC9B,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,MAAM,CAAC;IACf,UAAU,EAAE,MAAM,CAAC;IACnB,UAAU,EAAE,MAAM,CAAC;IACnB,MAAM,EAAE,MAAM,CAAC;IACf,IAAI,CAAC,EAAE,MAAM,EAAE,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,qBAAqB;IACpC,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,EAAE,EAAE,MAAM,CAAC;CACZ;AAED,MAAM,WAAW,gBAAgB;IAC/B,MAAM,EAAE,eAAe,CAAC;IACxB,aAAa,EAAE,qBAAqB,EAAE,CAAC;CACxC;AAaD,qBAAa,gBAAiB,SAAQ,KAAK;IAOhC,QAAQ,EAAE,MAAM;IANlB,cAAc,EAAE,MAAM,CAAC;IACvB,IAAI,EAAE,MAAM,CAAC;IACb,aAAa,CAAC,EAAE,MAAM,CAAC;gBAG5B,OAAO,EAAE,MAAM,EACR,QAAQ,EAAE,MAAM,EACvB,OAAO,CAAC,EAAE;QACR,cAAc,CAAC,EAAE,MAAM,CAAC;QACxB,IAAI,CAAC,EAAE,MAAM,CAAC;QACd,aAAa,CAAC,EAAE,MAAM,CAAC;KACxB;IASM,QAAQ;CAUlB;AAED,wBAAgB,sBAAsB,CACpC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,UAAU,EAAE,MAAM,GACjB,MAAM,EAAE,CA8CV;AAGD,wBAAgB,mBAAmB,CAAC,QAAQ,EAAE,MAAM,GAAG,gBAAgB,CAmJtE;AAED,wBAAgB,iBAAiB,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CASjE"}
+{"version":3,"file":"markdown.d.ts","sourceRoot":"","sources":["../../src/extractors/markdown.ts"],"names":[],"mappings":"AAsBA,MAAM,WAAW,eAAe;IAC9B,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,MAAM,CAAC;IACf,UAAU,EAAE,MAAM,CAAC;IACnB,UAAU,EAAE,MAAM,CAAC;IACnB,MAAM,EAAE,MAAM,CAAC;IACf,IAAI,CAAC,EAAE,MAAM,EAAE,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,qBAAqB;IACpC,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,EAAE,EAAE,MAAM,CAAC;CACZ;AAED,MAAM,WAAW,gBAAgB;IAC/B,MAAM,EAAE,eAAe,CAAC;IACxB,aAAa,EAAE,qBAAqB,EAAE,CAAC;CACxC;AAaD,qBAAa,gBAAiB,SAAQ,KAAK;IAOhC,QAAQ,EAAE,MAAM;IANlB,cAAc,EAAE,MAAM,CAAC;IACvB,IAAI,EAAE,MAAM,CAAC;IACb,aAAa,CAAC,EAAE,MAAM,CAAC;gBAG5B,OAAO,EAAE,MAAM,EACR,QAAQ,EAAE,MAAM,EACvB,OAAO,CAAC,EAAE;QACR,cAAc,CAAC,EAAE,MAAM,CAAC;QACxB,IAAI,CAAC,EAAE,MAAM,CAAC;QACd,aAAa,CAAC,EAAE,MAAM,CAAC;KACxB;IASM,QAAQ;CAUlB;AAED,wBAAgB,sBAAsB,CACpC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,UAAU,EAAE,MAAM,GACjB,MAAM,EAAE,CA8CV;AAGD,wBAAgB,mBAAmB,CAAC,QAAQ,EAAE,MAAM,GAAG,gBAAgB,CA4JtE;AAED,wBAAgB,iBAAiB,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CASjE"}

package/dist/extractors/markdown.js

@@ -101,7 +101,7 @@ export function extractFromMarkdown(filePath) {
         throw new FrontmatterError(`Failed to read file: ${error instanceof Error ? error.message : String(error)}`, filePath, { classification: "File Read Error" });
     }
     try {
-        const { data, content: body } = matter(content);
+        const { data } = matter(content);
         if (content.trim().startsWith("---")) {
             const parts = content.split("---");
             if (parts.length < 3) {
@@ -136,6 +136,14 @@ export function extractFromMarkdown(filePath) {
         const relationships = [];
         if (Array.isArray(data.links)) {
             for (const link of data.links) {
+                if (typeof link === "string") {
+                    relationships.push({
+                        type: "relates_to",
+                        from: id,
+                        to: link,
+                    });
+                    continue;
+                }
                 if (link &&
                     typeof link === "object" &&
                     typeof link.type === "string" &&

package/dist/public/extractors/symbols-coordinator.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"symbols-coordinator.d.ts","sourceRoot":"","sources":["../../../src/public/extractors/symbols-coordinator.ts"],"names":[],"mappings":"AAmBA,OAAO,EACL,uBAAuB,EACvB,KAAK,mBAAmB,GACzB,MAAM,yCAAyC,CAAC"}
+{"version":3,"file":"symbols-coordinator.d.ts","sourceRoot":"","sources":["../../../src/public/extractors/symbols-coordinator.ts"],"names":[],"mappings":"AAkBA,OAAO,EACL,uBAAuB,EACvB,KAAK,mBAAmB,GACzB,MAAM,yCAAyC,CAAC"}

package/dist/public/extractors/symbols-coordinator.js

@@ -14,6 +14,5 @@
 
  You should have received a copy of the GNU Affero General Public License
  along with this program.  If not, see <https://www.gnu.org/licenses/>.
-*/
-// Public re-export of symbols coordinator
+ */
 export { enrichSymbolCoordinates, } from "../../extractors/symbols-coordinator.js";

package/dist/public/prolog/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/public/prolog/index.ts"],"names":[],"mappings":"AAmBA,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/public/prolog/index.ts"],"names":[],"mappings":"AAkBA,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC"}

package/dist/public/prolog/index.js

@@ -14,6 +14,5 @@
 
  You should have received a copy of the GNU Affero General Public License
  along with this program.  If not, see <https://www.gnu.org/licenses/>.
-*/
-// Public re-export of PrologProcess
+ */
 export { PrologProcess } from "../../prolog.js";

package/dist/public/schemas/entity.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"entity.d.ts","sourceRoot":"","sources":["../../../src/public/schemas/entity.ts"],"names":[],"mappings":"AAoBA,QAAA,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAgEjB,CAAC;AAEF,eAAe,YAAY,CAAC"}
+{"version":3,"file":"entity.d.ts","sourceRoot":"","sources":["../../../src/public/schemas/entity.ts"],"names":[],"mappings":"AAkBA,QAAA,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAgEjB,CAAC;AAEF,eAAe,YAAY,CAAC"}

package/dist/public/schemas/entity.js

@@ -14,9 +14,7 @@
 
  You should have received a copy of the GNU Affero General Public License
  along with this program.  If not, see <https://www.gnu.org/licenses/>.
-*/
-// Public export of entity schema
-// Generated from entity.schema.json
+ */
 const entitySchema = {
     $id: "entity.schema.json",
     title: "Entity",

package/dist/public/schemas/relationship.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"relationship.d.ts","sourceRoot":"","sources":["../../../src/public/schemas/relationship.ts"],"names":[],"mappings":"AAoBA,QAAA,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAiCvB,CAAC;AAEF,eAAe,kBAAkB,CAAC"}
+{"version":3,"file":"relationship.d.ts","sourceRoot":"","sources":["../../../src/public/schemas/relationship.ts"],"names":[],"mappings":"AAkBA,QAAA,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAiCvB,CAAC;AAEF,eAAe,kBAAkB,CAAC"}

package/dist/public/schemas/relationship.js

@@ -14,9 +14,7 @@
 
  You should have received a copy of the GNU Affero General Public License
  along with this program.  If not, see <https://www.gnu.org/licenses/>.
-*/
-// Public export of relationship schema
-// Generated from relationship.schema.json
+ */
 const relationshipSchema = {
     $id: "relationship.schema.json",
     title: "Relationship",

package/dist/search-ranking.d.ts

@@ -0,0 +1,9 @@
+export interface SearchMatch {
+    entity: Record<string, unknown>;
+    score: number;
+    reasons: string[];
+    snippet?: string;
+}
+export declare function rankEntities(entities: Record<string, unknown>[], query: string, workspaceRoot: string): Promise<SearchMatch[]>;
+export declare function loadMarkdownBody(source: string, workspaceRoot: string): Promise<string | null>;
+//# sourceMappingURL=search-ranking.d.ts.map

package/dist/search-ranking.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"search-ranking.d.ts","sourceRoot":"","sources":["../src/search-ranking.ts"],"names":[],"mappings":"AAIA,MAAM,WAAW,WAAW;IAC1B,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAChC,KAAK,EAAE,MAAM,CAAC;IACd,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAGD,wBAAsB,YAAY,CAChC,QAAQ,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,EACnC,KAAK,EAAE,MAAM,EACb,aAAa,EAAE,MAAM,GACpB,OAAO,CAAC,WAAW,EAAE,CAAC,CAuBxB;AA2FD,wBAAsB,gBAAgB,CACpC,MAAM,EAAE,MAAM,EACd,aAAa,EAAE,MAAM,GACpB,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC,CA2BxB"}