kibi-cli 0.2.7 → 0.2.8

package/dist/commands/aggregated-checks.js

@@ -23,8 +23,7 @@ export async function runAggregatedChecks(prolog, rulesAllowlist, requireAdr = f
     try {
         const result = await prolog.query(query);
         if (!result.success) {
-            console.warn("Aggregated checks query failed, falling back to individual checks");
-            return [];
+            throw new Error(`Aggregated checks query failed: ${result.error || "Unknown error"}`);
         }
         let violationsDict;
         try {
@@ -39,8 +38,7 @@ export async function runAggregatedChecks(prolog, rulesAllowlist, requireAdr = f
             violationsDict = parsed;
         }
         catch (parseError) {
-            console.warn("Failed to parse violations JSON:", parseError);
-            return [];
+            throw new Error(`Failed to parse violations JSON: ${parseError instanceof Error ? parseError.message : String(parseError)}`);
         }
         for (const ruleViolations of Object.values(violationsDict)) {
             for (const v of ruleViolations) {
@@ -59,7 +57,7 @@ export async function runAggregatedChecks(prolog, rulesAllowlist, requireAdr = f
         return violations;
     }
     catch (error) {
-        console.warn("Error running aggregated checks:", error);
-        return [];
+        const message = error instanceof Error ? error.message : String(error);
+        throw new Error(`Error running aggregated checks: ${message}`);
     }
 }

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

@@ -1 +1 @@
-{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../src/commands/check.ts"],"names":[],"mappings":"AA2CA,MAAM,WAAW,YAAY;IAC3B,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;IAC3B,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,MAAM,WAAW,SAAS;IACxB,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,MAAM,CAAC;IACjB,WAAW,EAAE,MAAM,CAAC;IACpB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAGD,wBAAsB,YAAY,CAAC,OAAO,EAAE,YAAY,GAAG,OAAO,CAAC,IAAI,CAAC,CA0QvE"}
+{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../src/commands/check.ts"],"names":[],"mappings":"AAgDA,MAAM,WAAW,YAAY;IAC3B,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;IAC3B,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,MAAM,WAAW,SAAS;IACxB,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,MAAM,CAAC;IACjB,WAAW,EAAE,MAAM,CAAC;IACpB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAGD,wBAAsB,YAAY,CAAC,OAAO,EAAE,YAAY,GAAG,OAAO,CAAC,IAAI,CAAC,CA+RvE"}

package/dist/commands/check.js

@@ -16,24 +16,24 @@
  along with this program.  If not, see <https://www.gnu.org/licenses/>.
 */
 import * as path from "node:path";
+import { extractFromManifest } from "../extractors/manifest.js";
 import { PrologProcess } from "../prolog.js";
 import { escapeAtom } from "../prolog/codec.js";
 import { getStagedFiles } from "../traceability/git-staged.js";
 import { validateStagedMarkdown } from "../traceability/markdown-validate.js";
-import { extractSymbolsFromStagedFile } from "../traceability/symbol-extract.js";
+import { extractSymbolsFromStagedFile, } from "../traceability/symbol-extract.js";
 import { cleanupTempKb, consultOverlay, createOverlayFacts, createTempKb, } from "../traceability/temp-kb.js";
 import { formatViolations as formatStagedViolations, validateStagedSymbols, } from "../traceability/validate.js";
 import { loadConfig } from "../utils/config.js";
 import { RULES, getEffectiveRules, } from "../utils/rule-registry.js";
 import { runAggregatedChecks } from "./aggregated-checks.js";
 import { getCurrentBranch } from "./init-helpers.js";
+import { discoverSourceFiles } from "./sync/discovery.js";
 // implements REQ-006
 export async function checkCommand(options) {
     let prolog = null;
     let attached = false;
     try {
-        // Resolve KB path with priority:
-        // --kb-path > git branch --show-current > KIBI_BRANCH env > develop > main
         let resolvedKbPath = "";
         if (options.kbPath) {
             resolvedKbPath = options.kbPath;
@@ -54,13 +54,32 @@ export async function checkCommand(options) {
             // fallback to main if develop isn't present? keep path consistent
             resolvedKbPath = path.join(process.cwd(), ".kb/branches", branch || "main");
         }
-        // If --staged mode requested, run staged-symbol traceability gate.
-        // We skip creating the main prolog session entirely in this path.
         if (options.staged) {
             const minLinks = options.minLinks ? Number(options.minLinks) : 1;
             let tempCtx = null;
             try {
-                // Get staged files
+                const config = loadConfig(process.cwd());
+                const manifestLookup = new Map();
+                const { manifestFiles } = await discoverSourceFiles(process.cwd(), config.paths);
+                for (const manifestPath of manifestFiles) {
+                    try {
+                        const entries = extractFromManifest(manifestPath);
+                        for (const entry of entries) {
+                            // Prefer the per-symbol sourceFile; fall back to entity.source or manifest path
+                            const sourceFile = entry.sourceFile || entry.entity.source || manifestPath;
+                            const key = `${sourceFile}:${entry.entity.title}`;
+                            // Extract requirement links (implements relationships to REQ-*)
+                            const links = entry.relationships
+                                .filter((r) => r.type === "implements" &&
+                                r.to.match(/^[A-Z][A-Z0-9\-_]*$/))
+                                .map((r) => r.to);
+                            manifestLookup.set(key, { id: entry.entity.id, links });
+                        }
+                    }
+                    catch {
+                        // Ignore manifest parsing errors
+                    }
+                }
                 const stagedFiles = getStagedFiles();
                 if (!stagedFiles || stagedFiles.length === 0) {
                     console.log("No staged files found.");
@@ -89,7 +108,7 @@ export async function checkCommand(options) {
                 const allSymbols = [];
                 for (const f of codeFiles) {
                     try {
-                        const symbols = extractSymbolsFromStagedFile(f);
+                        const symbols = extractSymbolsFromStagedFile(f, manifestLookup);
                         if (symbols?.length) {
                             allSymbols.push(...symbols);
                         }
@@ -108,12 +127,10 @@ export async function checkCommand(options) {
                 }
                 // Create temp KB
                 tempCtx = await createTempKb(resolvedKbPath);
-                // Write overlay facts THEN consult so Prolog sees the changed_symbol facts
                 const overlayFacts = createOverlayFacts(allSymbols);
                 const fs = await import("node:fs/promises");
                 await fs.writeFile(tempCtx.overlayPath, overlayFacts, "utf8");
                 await consultOverlay(tempCtx);
-                // Validate staged symbols using the temp KB prolog session
                 const violationsRaw = await validateStagedSymbols({
                     minLinks,
                     prolog: tempCtx.prolog,
@@ -153,13 +170,11 @@ export async function checkCommand(options) {
         }
         attached = true;
         const violations = [];
-        // Load config to get rule enablement settings
         const config = loadConfig(process.cwd());
         const checksConfig = config.checks ?? {
             rules: Object.fromEntries(RULES.map((r) => [r.name, true])),
             symbolTraceability: { requireAdr: false },
         };
-        // Get effective rules based on config and CLI --rules filter
         const effectiveRules = getEffectiveRules(checksConfig.rules, options.rules);
         // Helper to conditionally run a check by name
         async function runCheck(name, fn, ...args) {
@@ -250,7 +265,6 @@ export async function checkCommand(options) {
 }
 async function checkMustPriorityCoverage(prolog) {
     const violations = [];
-    // Find all must-priority requirements
     const mustReqs = await findMustPriorityReqs(prolog);
     for (const reqId of mustReqs) {
         const entityResult = await prolog.query(`kb_entity('${reqId}', req, Props)`);
@@ -324,9 +338,7 @@ async function getAllEntityIds(prolog, type) {
 }
 async function checkNoDanglingRefs(prolog) {
     const violations = [];
-    // Get all entity IDs once
     const allEntityIds = new Set(await getAllEntityIds(prolog));
-    // Get all relationships by querying all known relationship types
     const relTypes = [
         "depends_on",
         "verified_by",
@@ -379,7 +391,6 @@ async function checkNoDanglingRefs(prolog) {
 }
 async function checkNoCycles(prolog) {
     const violations = [];
-    // Get all depends_on relationships
     const depsResult = await prolog.query("findall([From,To], kb_relationship(depends_on, From, To), Deps)");
     if (!depsResult.success || !depsResult.bindings.Deps) {
         return violations;
@@ -393,7 +404,6 @@ async function checkNoCycles(prolog) {
     if (!content) {
         return violations;
     }
-    // Build adjacency map
     const graph = new Map();
     const depMatches = content.matchAll(/\[([^,]+),([^\]]+)\]/g);
     for (const depMatch of depMatches) {
@@ -407,7 +417,6 @@ async function checkNoCycles(prolog) {
             fromList.push(to);
         }
     }
-    // DFS to detect cycles
     const visited = new Set();
     const recStack = new Set();
     function hasCycleDFS(node, path) {
@@ -429,7 +438,6 @@ async function checkNoCycles(prolog) {
         recStack.delete(node);
         return null;
     }
-    // Check each node for cycles
     for (const node of graph.keys()) {
         if (!visited.has(node)) {
             const cyclePath = hasCycleDFS(node, []);
@@ -472,15 +480,12 @@ async function checkRequiredFields(prolog, allEntityIds) {
     for (const entityId of allEntityIds) {
         const result = await prolog.query(`kb_entity('${entityId}', Type, Props)`);
         if (result.success && result.bindings.Props) {
-            // Parse properties list: [key1=value1, key2=value2, ...]
             const propsStr = result.bindings.Props;
             const propKeys = new Set();
-            // Extract keys from Props
             const keyMatches = propsStr.matchAll(/(\w+)\s*=/g);
             for (const match of keyMatches) {
                 propKeys.add(match[1]);
             }
-            // Check for missing required fields
             for (const field of required) {
                 if (!propKeys.has(field)) {
                     violations.push({
@@ -515,7 +520,6 @@ async function checkDeprecatedAdrs(prolog) {
         .split(",")
         .map((id) => id.trim().replace(/^'|'$/g, ""));
     for (const adrId of adrIds) {
-        // Get source for better error message
         const entityResult = await prolog.query(`kb_entity('${adrId}', adr, Props)`);
         let source = "";
         if (entityResult.success && entityResult.bindings.Props) {
@@ -585,10 +589,8 @@ async function checkSymbolTraceability(prolog, requireAdr) {
     if (!result.success || !result.bindings.Violations) {
         return violations;
     }
-    // Parse the violations from Prolog format
     const violationsStr = result.bindings.Violations;
     if (violationsStr && violationsStr !== "[]") {
-        // Parse each violation term
         const violationRegex = /violation\(([^,]+),'?([^',]+)'?,([^,]+),([^,]+),'?([^']*)'?\)/g;
         let match;
         do {

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/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/traceability/git-staged.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"git-staged.d.ts","sourceRoot":"","sources":["../../src/traceability/git-staged.ts"],"names":[],"mappings":"AAEA,MAAM,MAAM,MAAM,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,CAAC;AAE3C,MAAM,WAAW,SAAS;IACxB,KAAK,EAAE,MAAM,CAAC;IACd,GAAG,EAAE,MAAM,CAAC;CACb;AAED,MAAM,WAAW,UAAU;IACzB,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,CAAC;IACf,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,UAAU,EAAE,SAAS,EAAE,CAAC;IACxB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED,KAAK,MAAM,GAAG,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE;IAAE,QAAQ,EAAE,MAAM,CAAA;CAAE,KAAK,MAAM,CAAC;AAalE;;GAEG;AACH,wBAAgB,mBAAmB,CACjC,KAAK,EAAE,MAAM,GACZ,KAAK,CAAC;IAAE,MAAM,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,EAAE,CAAA;CAAE,CAAC,CAS5C;AAsCD;;GAEG;AACH,wBAAgB,kBAAkB,CAChC,QAAQ,EAAE,MAAM,EAChB,SAAS,UAAQ,GAChB,SAAS,EAAE,CAoBb;AAED;;GAEG;AACH,wBAAgB,cAAc,CAAC,IAAI,GAAE,MAAiB,GAAG,UAAU,EAAE,CA4FpE;AAED,eAAe,cAAc,CAAC"}
+{"version":3,"file":"git-staged.d.ts","sourceRoot":"","sources":["../../src/traceability/git-staged.ts"],"names":[],"mappings":"AAEA,MAAM,MAAM,MAAM,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,CAAC;AAE3C,MAAM,WAAW,SAAS;IACxB,KAAK,EAAE,MAAM,CAAC;IACd,GAAG,EAAE,MAAM,CAAC;CACb;AAED,MAAM,WAAW,UAAU;IACzB,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,CAAC;IACf,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,UAAU,EAAE,SAAS,EAAE,CAAC;IACxB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED,KAAK,MAAM,GAAG,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE;IAAE,QAAQ,EAAE,MAAM,CAAA;CAAE,KAAK,MAAM,CAAC;AAalE;;GAEG;AAEH,wBAAgB,mBAAmB,CACjC,KAAK,EAAE,MAAM,GACZ,KAAK,CAAC;IAAE,MAAM,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,EAAE,CAAA;CAAE,CAAC,CAwB5C;AAiDD;;GAEG;AACH,wBAAgB,kBAAkB,CAChC,QAAQ,EAAE,MAAM,EAChB,SAAS,UAAQ,GAChB,SAAS,EAAE,CAoBb;AAED;;GAEG;AAEH,wBAAgB,cAAc,CAAC,IAAI,GAAE,MAAiB,GAAG,UAAU,EAAE,CA6FpE;AAED,eAAe,cAAc,CAAC"}

package/dist/traceability/git-staged.js

@@ -13,16 +13,28 @@ function runGit(cmd, exec) {
 /**
  * Parse null-separated name-status output from git
  */
+// implements REQ-014
 export function parseNameStatusNull(input) {
     if (!input)
         return [];
     const entries = input.split("\0").filter(Boolean);
-    return entries.map((entry) => {
-        const cols = entry.split("\t");
-        const status = cols[0];
-        const parts = cols.slice(1);
-        return { status, parts };
-    });
+    const rows = [];
+    for (let i = 0; i < entries.length;) {
+        const entry = entries[i] ?? "";
+        if (entry.includes("\t")) {
+            const cols = entry.split("\t");
+            rows.push({ status: cols[0] ?? "", parts: cols.slice(1) });
+            i += 1;
+            continue;
+        }
+        const status = entry;
+        const isRenameOrCopy = /^[RC]\d*$/.test(status);
+        const partCount = isRenameOrCopy ? 2 : 1;
+        const parts = entries.slice(i + 1, i + 1 + partCount);
+        rows.push({ status, parts });
+        i += 1 + partCount;
+    }
+    return rows;
 }
 const SUPPORTED_EXT = new Set([
     ".ts",
@@ -34,6 +46,7 @@ const SUPPORTED_EXT = new Set([
     ".mjs",
     ".cjs",
 ]);
+const SUPPORTED_MANIFEST = new Set(["symbols.yaml", "symbols.yml"]);
 const ENTITY_MARKDOWN_DIRS = ["/requirements/", "/scenarios/", "/tests/"];
 function shouldLogTraceDebug() {
     return Boolean(process.env.KIBI_TRACE || process.env.KIBI_DEBUG);
@@ -57,6 +70,16 @@ function isEntityMarkdown(p) {
     }
     return false;
 }
+function isManifestFile(p) {
+    const base = p.split(/[\/]/).pop();
+    if (!base)
+        return false;
+    for (const name of SUPPORTED_MANIFEST) {
+        if (base === name)
+            return true;
+    }
+    return false;
+}
 /**
  * Parse unified diff hunks (new-file coordinates) from git diff output
  */
@@ -86,6 +109,7 @@ export function parseHunksFromDiff(diffText, isNewFile = false) {
 /**
  * Get staged files with statuses, hunks and content.
  */
+// implements REQ-014
 export function getStagedFiles(exec = execSync) {
     // 1. get staged name-status -z
     let nameStatus;
@@ -115,7 +139,9 @@ export function getStagedFiles(exec = execSync) {
                 path = entry.parts[1];
             }
         }
-        if (!hasSupportedExt(path) && !isEntityMarkdown(path)) {
+        if (!hasSupportedExt(path) &&
+            !isEntityMarkdown(path) &&
+            !isManifestFile(path)) {
             if (shouldLogTraceDebug()) {
                 console.debug(`Skipping unsupported extension: ${path}`);
             }

package/dist/traceability/symbol-extract.d.ts

@@ -11,5 +11,10 @@ export interface ExtractedSymbol {
     hunkRanges: HunkRange[];
     reqLinks: string[];
 }
-export declare function extractSymbolsFromStagedFile(stagedFile: StagedFile): ExtractedSymbol[];
+export interface ManifestLookupEntry {
+    id: string;
+    links?: string[];
+}
+export type ManifestLookup = Map<string, ManifestLookupEntry>;
+export declare function extractSymbolsFromStagedFile(stagedFile: StagedFile, manifestLookup?: ManifestLookup): ExtractedSymbol[];
 //# sourceMappingURL=symbol-extract.d.ts.map

package/dist/traceability/symbol-extract.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"symbol-extract.d.ts","sourceRoot":"","sources":["../../src/traceability/symbol-extract.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,iBAAiB,CAAC;AAE7D,MAAM,WAAW,eAAe;IAC9B,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,UAAU,GAAG,OAAO,GAAG,UAAU,GAAG,MAAM,GAAG,SAAS,CAAC;IAC7D,QAAQ,EAAE;QACR,IAAI,EAAE,MAAM,CAAC;QACb,SAAS,EAAE,MAAM,CAAC;QAClB,OAAO,EAAE,MAAM,CAAC;KACjB,CAAC;IACF,UAAU,EAAE,SAAS,EAAE,CAAC;IACxB,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AA0DD,wBAAgB,4BAA4B,CAC1C,UAAU,EAAE,UAAU,GACrB,eAAe,EAAE,CAuLnB"}
+{"version":3,"file":"symbol-extract.d.ts","sourceRoot":"","sources":["../../src/traceability/symbol-extract.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,iBAAiB,CAAC;AAE7D,MAAM,WAAW,eAAe;IAC9B,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,UAAU,GAAG,OAAO,GAAG,UAAU,GAAG,MAAM,GAAG,SAAS,CAAC;IAC7D,QAAQ,EAAE;QACR,IAAI,EAAE,MAAM,CAAC;QACb,SAAS,EAAE,MAAM,CAAC;QAClB,OAAO,EAAE,MAAM,CAAC;KACjB,CAAC;IACF,UAAU,EAAE,SAAS,EAAE,CAAC;IACxB,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAED,MAAM,WAAW,mBAAmB;IAClC,EAAE,EAAE,MAAM,CAAC;IACX,KAAK,CAAC,EAAE,MAAM,EAAE,CAAC;CAClB;AAED,MAAM,MAAM,cAAc,GAAG,GAAG,CAAC,MAAM,EAAE,mBAAmB,CAAC,CAAC;AA4D9D,wBAAgB,4BAA4B,CAC1C,UAAU,EAAE,UAAU,EACtB,cAAc,CAAC,EAAE,cAAc,GAC9B,eAAe,EAAE,CA+MnB"}

package/dist/traceability/symbol-extract.js

@@ -28,7 +28,10 @@ function parseReqDirectives(text) {
     const regex = new RegExp(`implements\\s*:?\\s*(${REQ_ID}(?:\\s*,\\s*${REQ_ID})*)\\s*$`, "gim");
     const reqs = new Set();
     let m;
-    while ((m = regex.exec(text))) {
+    while (true) {
+        m = regex.exec(text);
+        if (!m)
+            break;
         const list = m[1];
         for (const part of list.split(/[,\s]+/)) {
             const p = part.trim();
@@ -42,9 +45,9 @@ function parseReqDirectives(text) {
 function rangesIntersect(aStart, aEnd, bStart, bEnd) {
     return aStart <= bEnd && bStart <= aEnd;
 }
-export function extractSymbolsFromStagedFile(stagedFile) {
+export function extractSymbolsFromStagedFile(stagedFile, manifestLookup) {
     const content = stagedFile.content ?? "";
-    const sha = computeContentSha(content + "|" + stagedFile.path);
+    const sha = computeContentSha(`${content}|${stagedFile.path}`);
     // TTL cache lookup
     const now = Date.now();
     let cached = sourceFileCache.get(sha);
@@ -52,7 +55,7 @@ export function extractSymbolsFromStagedFile(stagedFile) {
         // create or recreate SourceFile in project (in-memory)
         try {
             const scriptKind = chooseScriptKind(stagedFile.path);
-            const sf = project.createSourceFile(stagedFile.path + "::staged", content, {
+            const sf = project.createSourceFile(`${stagedFile.path}::staged`, content, {
                 overwrite: true,
                 scriptKind,
             });
@@ -85,13 +88,13 @@ export function extractSymbolsFromStagedFile(stagedFile) {
             const start = nameNode ? nameNode.getStart() : fn.getStart();
             const end = fn.getEnd();
             const span = getSpan(start, end);
-            const reqLinks = parseReqDirectives(fn.getFullText() +
-                "\n" +
-                fn
-                    .getJsDocs()
-                    .map((d) => d.getFullText())
-                    .join("\n"));
-            const id = resolveSymbolId(stagedFile.path, name);
+            const reqLinks = parseReqDirectives(`${fn.getFullText()}\n${fn
+                .getJsDocs()
+                .map((d) => d.getFullText())
+                .join("\n")}`);
+            const { id, reqLinks: manifestLinks } = resolveSymbolId(stagedFile.path, name, manifestLookup);
+            // Merge manifest links with inline directive links (manifest links as fallback)
+            const mergedReqLinks = reqLinks.length > 0 ? reqLinks : (manifestLinks ?? []);
             results.push({
                 id,
                 name,
@@ -102,7 +105,7 @@ export function extractSymbolsFromStagedFile(stagedFile) {
                     endLine: span.endLine,
                 },
                 hunkRanges: intersectingHunks(span.startLine, span.endLine, stagedFile.hunkRanges),
-                reqLinks,
+                reqLinks: mergedReqLinks,
             });
         }
         catch { }
@@ -116,13 +119,13 @@ export function extractSymbolsFromStagedFile(stagedFile) {
             const start = cls.getNameNode()?.getStart() ?? cls.getStart();
             const end = cls.getEnd();
             const span = getSpan(start, end);
-            const reqLinks = parseReqDirectives(cls.getText() +
-                "\n" +
-                cls
-                    .getJsDocs()
-                    .map((d) => d.getFullText())
-                    .join("\n"));
-            const id = resolveSymbolId(stagedFile.path, name);
+            const reqLinks = parseReqDirectives(`${cls.getText()}\n${cls
+                .getJsDocs()
+                .map((d) => d.getFullText())
+                .join("\n")}`);
+            const { id, reqLinks: manifestLinks } = resolveSymbolId(stagedFile.path, name, manifestLookup);
+            // Merge manifest links with inline directive links (manifest links as fallback)
+            const mergedReqLinks = reqLinks.length > 0 ? reqLinks : (manifestLinks ?? []);
             results.push({
                 id,
                 name,
@@ -133,7 +136,7 @@ export function extractSymbolsFromStagedFile(stagedFile) {
                     endLine: span.endLine,
                 },
                 hunkRanges: intersectingHunks(span.startLine, span.endLine, stagedFile.hunkRanges),
-                reqLinks,
+                reqLinks: mergedReqLinks,
             });
         }
         catch { }
@@ -148,7 +151,9 @@ export function extractSymbolsFromStagedFile(stagedFile) {
             const end = en.getEnd();
             const span = getSpan(start, end);
             const reqLinks = parseReqDirectives(en.getText());
-            const id = resolveSymbolId(stagedFile.path, name);
+            const { id, reqLinks: manifestLinks } = resolveSymbolId(stagedFile.path, name, manifestLookup);
+            // Merge manifest links with inline directive links (manifest links as fallback)
+            const mergedReqLinks = reqLinks.length > 0 ? reqLinks : (manifestLinks ?? []);
             results.push({
                 id,
                 name,
@@ -159,7 +164,7 @@ export function extractSymbolsFromStagedFile(stagedFile) {
                     endLine: span.endLine,
                 },
                 hunkRanges: intersectingHunks(span.startLine, span.endLine, stagedFile.hunkRanges),
-                reqLinks,
+                reqLinks: mergedReqLinks,
             });
         }
         catch { }
@@ -175,7 +180,9 @@ export function extractSymbolsFromStagedFile(stagedFile) {
                 const end = decl.getEnd();
                 const span = getSpan(start, end);
                 const reqLinks = parseReqDirectives(decl.getText());
-                const id = resolveSymbolId(stagedFile.path, name);
+                const { id, reqLinks: manifestLinks } = resolveSymbolId(stagedFile.path, name, manifestLookup);
+                // Merge manifest links with inline directive links (manifest links as fallback)
+                const mergedReqLinks = reqLinks.length > 0 ? reqLinks : (manifestLinks ?? []);
                 results.push({
                     id,
                     name,
@@ -186,7 +193,7 @@ export function extractSymbolsFromStagedFile(stagedFile) {
                         endLine: span.endLine,
                     },
                     hunkRanges: intersectingHunks(span.startLine, span.endLine, stagedFile.hunkRanges),
-                    reqLinks,
+                    reqLinks: mergedReqLinks,
                 });
             }
             catch { }
@@ -208,21 +215,42 @@ function intersectingHunks(startLine, endLine, hunks) {
     }
     return out;
 }
-function resolveSymbolId(filePath, name) {
+function resolveSymbolId(filePath, name, manifestLookup) {
+    // First, check the provided manifest lookup if available
+    if (manifestLookup) {
+        // Normalize the source file path for consistent lookup
+        const normalizedSource = filePath.startsWith("/")
+            ? filePath
+            : `${filePath}`;
+        const lookupKey = `${normalizedSource}:${name}`;
+        const entry = manifestLookup.get(lookupKey);
+        if (entry) {
+            return { id: entry.id, reqLinks: entry.links };
+        }
+    }
+    // Fallback: attempt to read manifest entries from a local symbols.yaml (best-effort)
     try {
-        // attempt to read manifest entries for explicit id (best-effort)
-        // extractFromManifest expects a file path; if manifest not present it will throw — catch it
-        const ents = extractFromManifest(filePath);
-        for (const e of ents) {
-            if (e.entity.title === name)
-                return e.entity.id;
+        // Try to find a symbols.yaml in the same directory as the file
+        const dir = filePath.substring(0, filePath.lastIndexOf("/"));
+        if (dir) {
+            const manifestPath = `${dir}/symbols.yaml`;
+            const ents = extractFromManifest(manifestPath);
+            for (const e of ents) {
+                if (e.entity.title === name) {
+                    // Extract requirement links from relationships
+                    const reqLinks = e.relationships
+                        .filter((r) => r.type === "implements" && r.to.match(/^[A-Z][A-Z0-9\-_]*$/))
+                        .map((r) => r.to);
+                    return { id: e.entity.id, reqLinks };
+                }
+            }
         }
     }
     catch {
-        // ignore
+        // ignore - no local manifest or parse error
     }
-    // deterministic id: sha(file:path:name)
+    // Final fallback: deterministic id: sha(file:path:name)
     const h = createHash("sha256");
     h.update(`${filePath}:${name}`);
-    return h.digest("hex").slice(0, 16);
+    return { id: h.digest("hex").slice(0, 16) };
 }

package/dist/traceability/temp-kb.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"temp-kb.d.ts","sourceRoot":"","sources":["../../src/traceability/temp-kb.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,aAAa,EAAE,MAAM,cAAc,CAAC;AAC7C,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAC;AAExD,MAAM,WAAW,aAAa;IAC5B,OAAO,EAAE,MAAM,CAAC;IAChB,MAAM,EAAE,MAAM,CAAC;IACf,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,aAAa,CAAC;CACvB;AAmDD,iBAAe,cAAc,CAAC,GAAG,EAAE,aAAa,GAAG,OAAO,CAAC,IAAI,CAAC,CAe/D;AAED,OAAO,EAAE,cAAc,EAAE,CAAC;AAE1B,wBAAsB,YAAY,CAAC,UAAU,EAAE,MAAM,GAAG,OAAO,CAAC,aAAa,CAAC,CA2C7E;AAED,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,eAAe,EAAE,GAAG,MAAM,CAkBrE;AAED,wBAAsB,aAAa,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CA2BlE"}
+{"version":3,"file":"temp-kb.d.ts","sourceRoot":"","sources":["../../src/traceability/temp-kb.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,aAAa,EAAE,MAAM,cAAc,CAAC;AAC7C,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAC;AAExD,MAAM,WAAW,aAAa;IAC5B,OAAO,EAAE,MAAM,CAAC;IAChB,MAAM,EAAE,MAAM,CAAC;IACf,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,aAAa,CAAC;CACvB;AAmDD,iBAAe,cAAc,CAAC,GAAG,EAAE,aAAa,GAAG,OAAO,CAAC,IAAI,CAAC,CAe/D;AAED,OAAO,EAAE,cAAc,EAAE,CAAC;AAE1B,wBAAsB,YAAY,CAAC,UAAU,EAAE,MAAM,GAAG,OAAO,CAAC,aAAa,CAAC,CA2C7E;AAGD,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,eAAe,EAAE,GAAG,MAAM,CAkBrE;AAED,wBAAsB,aAAa,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CA2BlE"}

package/dist/traceability/temp-kb.js

@@ -82,14 +82,15 @@ export async function createTempKb(baseKbPath) {
     trace(`temporary KB ready at ${kbPath}`);
     return ctx;
 }
+// implements REQ-014
 export function createOverlayFacts(symbols) {
     const lines = [];
     for (const symbol of symbols) {
-        lines.push(`changed_symbol(${escapePrologAtom(symbol.id)}).`);
-        lines.push(`changed_symbol_loc(${escapePrologAtom(symbol.id)}, ${escapePrologAtom(symbol.location.file)}, ${symbol.location.startLine}, 0, ${escapePrologAtom(symbol.name)}).`);
+        lines.push(`kb:changed_symbol(${escapePrologAtom(symbol.id)}).`);
+        lines.push(`kb:changed_symbol_loc(${escapePrologAtom(symbol.id)}, ${escapePrologAtom(symbol.location.file)}, ${symbol.location.startLine}, 0, ${escapePrologAtom(symbol.name)}).`);
         // Emit overlay facts for requirement links from code-comment directives.
         for (const reqId of symbol.reqLinks) {
-            lines.push(`changed_symbol_req(${escapePrologAtom(symbol.id)}, ${escapePrologAtom(reqId)}).`);
+            lines.push(`kb:changed_symbol_req(${escapePrologAtom(symbol.id)}, ${escapePrologAtom(reqId)}).`);
         }
     }
     return lines.join("\n");

package/dist/traceability/validate.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"validate.d.ts","sourceRoot":"","sources":["../../src/traceability/validate.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,cAAc,CAAC;AAElD,MAAM,WAAW,iBAAiB;IAChC,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,aAAa,CAAC;CACvB;AAED,MAAM,WAAW,SAAS;IACxB,QAAQ,EAAE,MAAM,CAAC;IACjB,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,CAAC;IACf,YAAY,EAAE,MAAM,CAAC;IACrB,aAAa,EAAE,MAAM,CAAC;CACvB;AAgHD,wBAAsB,qBAAqB,CACzC,OAAO,EAAE,iBAAiB,GACzB,OAAO,CAAC,SAAS,EAAE,CAAC,CAqCtB;AAED,wBAAgB,gBAAgB,CAAC,UAAU,EAAE,SAAS,EAAE,GAAG,MAAM,CAiBhE"}
+{"version":3,"file":"validate.d.ts","sourceRoot":"","sources":["../../src/traceability/validate.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,cAAc,CAAC;AAElD,MAAM,WAAW,iBAAiB;IAChC,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,aAAa,CAAC;CACvB;AAED,MAAM,WAAW,SAAS;IACxB,QAAQ,EAAE,MAAM,CAAC;IACjB,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,CAAC;IACf,YAAY,EAAE,MAAM,CAAC;IACrB,aAAa,EAAE,MAAM,CAAC;CACvB;AAiHD,wBAAsB,qBAAqB,CACzC,OAAO,EAAE,iBAAiB,GACzB,OAAO,CAAC,SAAS,EAAE,CAAC,CAqCtB;AAED,wBAAgB,gBAAgB,CAAC,UAAU,EAAE,SAAS,EAAE,GAAG,MAAM,CAiBhE"}

package/dist/traceability/validate.js

@@ -1,10 +1,10 @@
-function unquoteAtom(v) {
+function unquoteAtom(value) {
     // remove surrounding single quotes and unescape doubled quotes
-    v = v.trim();
-    if (v.startsWith("'") && v.endsWith("'")) {
-        v = v.slice(1, -1).replace(/''/g, "'");
+    const trimmed = value.trim();
+    if (trimmed.startsWith("'") && trimmed.endsWith("'")) {
+        return trimmed.slice(1, -1).replace(/''/g, "'");
     }
-    return v;
+    return trimmed;
 }
 function splitTopLevelComma(s) {
     const parts = [];
@@ -98,14 +98,15 @@ function parsePrologListOfLists(value) {
     }
     return out;
 }
+// implements REQ-014
 export async function validateStagedSymbols(options) {
     const { minLinks, prolog } = options;
-    const goal = `findall([Sym,Count,File,Line,Col,Name], changed_symbol_violation(Sym, ${minLinks}, Count, File, Line, Col, Name), Rows)`;
+    const goal = `findall([Sym,Count,File,Line,Col,Name], kb:changed_symbol_violation(Sym, ${minLinks}, Count, File, Line, Col, Name), Rows)`;
     const res = await prolog.query(goal);
     if (!res.success) {
         throw new Error(`Prolog query failed: ${res.error || "unknown error"}`);
     }
-    const rowsRaw = res.bindings["Rows"] ?? "[]";
+    const rowsRaw = res.bindings.Rows ?? "[]";
     const lists = parsePrologListOfLists(rowsRaw);
     const violations = [];
     for (const row of lists) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "kibi-cli",
-  "version": "0.2.7",
+  "version": "0.2.8",
   "type": "module",
   "description": "Kibi CLI for knowledge base management",
   "engines": {
@@ -71,6 +71,10 @@
     "kibi-core": "^0.1.10",
     "ts-morph": "^23.0.0"
   },
+  "devDependencies": {
+    "@types/node": "latest",
+    "typescript": "^5.7.0"
+  },
   "license": "AGPL-3.0-or-later",
   "author": "Piotr Franczyk",
   "repository": {

package/src/public/extractors/symbols-coordinator.ts

@@ -14,9 +14,8 @@
 
  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,
   type ManifestSymbolEntry,

package/src/public/prolog/index.ts

@@ -14,7 +14,6 @@
 
  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/src/public/schemas/entity.ts

@@ -14,10 +14,8 @@
 
  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/src/public/schemas/relationship.ts

@@ -14,10 +14,8 @@
 
  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",