kibi-cli 2.17.0 → 2.18.0

package/dist/cli-register-proof.js

@@ -162,7 +162,15 @@ function renderInspection(result) {
     if (inspection.ciWorkflows.length > 0)
         lines.push(`CI workflows: ${inspection.ciWorkflows.join(", ")}`);
     lines.push("");
-    lines.push(`Current integration: ${inspection.currentIntegration ?? "none"}`);
+    const configured = inspection.currentIntegrations ?? [];
+    if (configured.length === 0) {
+        lines.push(`Current integration: ${inspection.currentIntegration ?? "none"}`);
+    }
+    else {
+        lines.push("Current integrations:");
+        for (const entry of configured)
+            lines.push(`  ${entry.id} (${entry.producer}: ${entry.command.join(" ")})`);
+    }
     lines.push("");
     lines.push(`Recommendation: ${inspection.recommendation}`);
     if (inspection.missing.length > 0) {

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

@@ -1 +1 @@
-{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../src/commands/doctor.ts"],"names":[],"mappings":"AA2FA,MAAM,WAAW,aAAa;IAC5B,MAAM,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;CAC3B;AAGD,wBAAsB,aAAa,CACjC,OAAO,GAAE,aAAkB,GAC1B,OAAO,CAAC;IAAE,QAAQ,EAAE,MAAM,CAAA;CAAE,CAAC,CAmH/B;AAED,wBAAsB,4BAA4B,CAChD,IAAI,GAAE,MAAM,OAAO,CAAC;IAAE,gBAAgB,CAAC,EAAE,OAAO,CAAA;CAAE,CACT,GACxC,OAAO,CAAC,OAAO,CAAC,CAOlB;AAED,wBAAsB,uBAAuB,CAC3C,OAAO,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;;;;;;;;;;;;;;;;MAkE3C;AAkGD,wBAAgB,qBAAqB,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAGzE;AAED,wBAAgB,2BAA2B,CACzC,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,GACX,MAAM,GAAG,SAAS,CAepB"}
+{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../src/commands/doctor.ts"],"names":[],"mappings":"AA4FA,MAAM,WAAW,aAAa;IAC5B,MAAM,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;CAC3B;AAGD,wBAAsB,aAAa,CACjC,OAAO,GAAE,aAAkB,GAC1B,OAAO,CAAC;IAAE,QAAQ,EAAE,MAAM,CAAA;CAAE,CAAC,CAmH/B;AAED,wBAAsB,4BAA4B,CAChD,IAAI,GAAE,MAAM,OAAO,CAAC;IAAE,gBAAgB,CAAC,EAAE,OAAO,CAAA;CAAE,CACT,GACxC,OAAO,CAAC,OAAO,CAAC,CAOlB;AAED,wBAAsB,uBAAuB,CAC3C,OAAO,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;;;;;;;;;;;;;;;;MAkE3C;AAkGD,wBAAgB,qBAAqB,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAGzE;AAED,wBAAgB,2BAA2B,CACzC,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,GACX,MAAM,GAAG,SAAS,CAepB"}

package/dist/commands/doctor.js

@@ -26,7 +26,7 @@ import { describeConfiguredCapabilityPlugins, readProjectKibiConfig, } from "../
 import { SwiplResolutionError, inspectSwiplBundle, probeRequiredLibraries, resolveSwipl, } from "../prolog/swipl-resolver.js";
 import { buildMigrationPlan, migrationAction, } from "../public/operations/migration-plan.js";
 import { resolveBranchAttachment, resolveReadBranchAttachment, } from "../utils/branch-resolver.js";
-import { branchStoreCompilation, inspectBranchStore, uncompiledBranchStoreReason, } from "../utils/branch-store.js";
+import { branchStoreCompilation, inspectBranchStore, storeLockTakeoverReason, uncompiledBranchStoreReason, } from "../utils/branch-store.js";
 import { resolveGitRepository, } from "../utils/git-repository-context.js";
 import { readKbManifestStatus } from "../utils/kb-manifest.js";
 import { hasManagedHooks, outdatedManagedHooks } from "./init-helpers.js";
@@ -692,11 +692,17 @@ function checkBranchStore() {
         };
     }
     const compilation = branchStoreCompilation(store);
+    // implements REQ-core-journaled-engine-persistence
+    const takeover = storeLockTakeoverReason(store.path);
     if (compilation.compiled) {
         return {
             passed: true,
-            message: `Compiled for ${branch}${compilation.generation ? ` (${compilation.generation})` : ""}`,
-            details: { ...details, generation: compilation.generation },
+            message: `Compiled for ${branch}${compilation.generation ? ` (${compilation.generation})` : ""}${takeover ? `. ${String(takeover.detail)}` : ""}`,
+            details: {
+                ...details,
+                generation: compilation.generation,
+                ...(takeover ? { lockTakeover: takeover } : {}),
+            },
         };
     }
     const reason = uncompiledBranchStoreReason(workspaceRoot, store, branch);

package/dist/commands/sync/untracked-targets.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"untracked-targets.d.ts","sourceRoot":"","sources":["../../../src/commands/sync/untracked-targets.ts"],"names":[],"mappings":"AAsBA,UAAU,oBAAoB;IAC5B,YAAY,EAAE,CACZ,IAAI,EAAE,MAAM,EACZ,IAAI,EAAE,SAAS,MAAM,EAAE,EACvB,OAAO,EAAE;QAAE,QAAQ,EAAE,MAAM,CAAC;QAAC,SAAS,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,KAC5D,MAAM,CAAC;IACZ,UAAU,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC;IACtC,YAAY,EAAE,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,KAAK,MAAM,CAAC;CAC1D;AAQD;;;;;;;;;;;GAWG;AAEH,wBAAgB,4BAA4B,CAC1C,aAAa,EAAE,MAAM,EACrB,UAAU,EAAE,SAAS,MAAM,EAAE,EAC7B,IAAI,GAAE,OAAO,CAAC,oBAAoB,CAAM,GACvC,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAiDrB"}
+{"version":3,"file":"untracked-targets.d.ts","sourceRoot":"","sources":["../../../src/commands/sync/untracked-targets.ts"],"names":[],"mappings":"AAyBA,UAAU,oBAAoB;IAC5B,YAAY,EAAE,CACZ,IAAI,EAAE,MAAM,EACZ,IAAI,EAAE,SAAS,MAAM,EAAE,EACvB,OAAO,EAAE;QAAE,QAAQ,EAAE,MAAM,CAAC;QAAC,SAAS,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,KAC5D,MAAM,CAAC;IACZ,UAAU,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC;IACtC,YAAY,EAAE,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,KAAK,MAAM,CAAC;CAC1D;AAQD;;;;;;;;;;;GAWG;AAEH,wBAAgB,4BAA4B,CAC1C,aAAa,EAAE,MAAM,EACrB,UAAU,EAAE,SAAS,MAAM,EAAE,EAC7B,IAAI,GAAE,OAAO,CAAC,oBAAoB,CAAM,GACvC,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAsDrB"}

package/dist/commands/sync/untracked-targets.js

@@ -16,8 +16,11 @@
  along with this program.  If not, see <https://www.gnu.org/licenses/>.
  */
 import { execFileSync } from "node:child_process";
+import { createHash } from "node:crypto";
 import { existsSync, readFileSync } from "node:fs";
 import * as path from "node:path";
+import { load as parseYAML } from "js-yaml";
+import { isSymbolsManifestPath } from "../../utils/kb-paths.js";
 const defaultDeps = {
     execFileSync: (file, args, options) => execFileSync(file, args, options),
     existsSync,
@@ -62,11 +65,20 @@ export function findUntrackedDocumentMatches(workspaceRoot, missingIds, deps = {
     for (const relative of untracked) {
         if (remaining.size === 0)
             break;
-        if (!relative.endsWith(".md"))
+        const normalized = relative.replaceAll("\\", "/");
+        const manifest = isSymbolsManifestPath(normalized);
+        if (!normalized.endsWith(".md") && !manifest)
             continue;
-        const absolute = path.resolve(workspaceRoot, relative.replaceAll("\\", "/"));
+        const absolute = path.resolve(workspaceRoot, normalized);
         if (!resolved.existsSync(absolute))
             continue;
+        const workspaceRelative = path
+            .relative(workspaceRoot, absolute)
+            .replaceAll("\\", "/");
+        // A pending-source receipt makes an untracked file visible to sync, so
+        // the file cannot be why an id is missing.
+        if (existsSync(pendingReceiptFor(workspaceRoot, workspaceRelative)))
+            continue;
         let content;
         try {
             content = resolved.readFileSync(absolute, "utf8");
@@ -74,17 +86,35 @@ export function findUntrackedDocumentMatches(workspaceRoot, missingIds, deps = {
         catch {
             continue;
         }
-        const id = frontmatterId(content);
-        if (id !== null && remaining.has(id)) {
-            const workspaceRelative = path
-                .relative(workspaceRoot, absolute)
-                .replaceAll("\\", "/");
-            matches.set(id, workspaceRelative);
-            remaining.delete(id);
+        const ids = manifest ? manifestIds(content) : [frontmatterId(content)];
+        for (const id of ids) {
+            if (id !== null && remaining.has(id)) {
+                matches.set(id, workspaceRelative);
+                remaining.delete(id);
+            }
         }
     }
     return matches;
 }
+/** Where kb_upsert records the pending-source receipt of `relative`. */
+function pendingReceiptFor(workspaceRoot, relative) {
+    return path.join(workspaceRoot, ".kb", "recovery", "pending-sources", `${createHash("sha256").update(relative).digest("hex")}.json`);
+}
+/** Symbol ids declared by an untracked symbols manifest. */
+function manifestIds(content) {
+    try {
+        const parsed = parseYAML(content);
+        const symbols = Array.isArray(parsed?.symbols) ? parsed.symbols : [];
+        return symbols.flatMap((symbol) => symbol !== null &&
+            typeof symbol === "object" &&
+            typeof symbol.id === "string"
+            ? [symbol.id]
+            : []);
+    }
+    catch {
+        return [];
+    }
+}
 /**
  * Extract `id:` from a markdown document's YAML frontmatter (the first
  * `---` block). Documents whose id never appears in the frontmatter region

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

@@ -1 +1 @@
-{"version":3,"file":"sync.d.ts","sourceRoot":"","sources":["../../src/commands/sync.ts"],"names":[],"mappings":"AA6BA,OAAO,KAAK,EAAE,UAAU,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AA6BjE,OAAO,EAEL,yBAAyB,EAE1B,MAAM,gDAAgD,CAAC;AAGxD,OAAO,EAAE,aAAa,EAAE,MAAM,cAAc,CAAC;AAC7C,OAAO,EACL,KAAK,gBAAgB,EAGtB,MAAM,6BAA6B,CAAC;AAyBrC,OAAO,KAAK,EAAE,4BAA4B,EAAE,MAAM,qBAAqB,CAAC;AA2BxE,qBAAa,SAAU,SAAQ,KAAK;gBACtB,OAAO,EAAE,MAAM;CAI5B;AAmCD,wBAAgB,wBAAwB,CACtC,aAAa,EAAE,MAAM,EACrB,gBAAgB,EAAE,MAAM,EACxB,4BAA4B,UAAQ,EACpC,4BAA4B,GAAE,4BAA4B,EAAO,GAChE,MAAM,EAAE,CAuGV;AAqDD,MAAM,WAAW,UAAW,SAAQ,WAAW;IAC7C,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,UAAU,yBAAyB;IACjC,aAAa,EAAE,MAAM,CAAC;IACtB,QAAQ,EAAE,MAAM,CAAC;IACjB,OAAO,EAAE,OAAO,CAAC;IACjB,WAAW,EAAE,MAAM,CAAC;IACpB,YAAY,EAAE,OAAO,CAAC;CACvB;AAED,UAAU,kBAAkB;IAC1B,WAAW,CAAC,EAAE,CAAC,OAAO,EAAE,yBAAyB,KAAK,OAAO,CAAC,IAAI,CAAC,GAAG,IAAI,CAAC;IAC3E,UAAU,CAAC,EAAE,CACX,OAAO,EAAE,yBAAyB,GAAG;QAAE,UAAU,EAAE,OAAO,CAAA;KAAE,KACzD,OAAO,CAAC,IAAI,CAAC,GAAG,IAAI,CAAC;IAC1B,YAAY,CAAC,EAAE,CAAC,OAAO,EAAE;QAAE,OAAO,EAAE,MAAM,CAAA;KAAE,KAAK,aAAa,CAAC;IAC/D,yBAAyB,CAAC,EAAE,OAAO,yBAAyB,CAAC;CAC9D;AA6DD,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,OAAO,GAAG,IAAI,CAGvE;AAGD,wBAAgB,2BAA2B,CACzC,IAAI,EAAE,MAAM,EACZ,KAAK,EAAE,MAAM,IAAI,GAChB,IAAI,CAMN;AAED,wBAAgB,4BAA4B,CAC1C,WAAW,EAAE,UAAU,EAAE,EACzB,QAAQ,EAAE,OAAO,EACjB,OAAO,EAAE,OAAO,EAChB,aAAa,EAAE,MAAM,EACrB,QAAQ,EAAE,MAAM,GACf,IAAI,CAIN;AAED,wBAAgB,0BAA0B,CAAC,MAAM,EAAE;IACjD,OAAO,EAAE,OAAO,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB,GAAG,IAAI,CAMP;AAED,wBAAgB,iCAAiC,CAC/C,WAAW,EAAE,UAAU,EAAE,EACzB,oBAAoB,EAAE,OAAO,EAC7B,iBAAiB,EAAE,MAAM,EACzB,WAAW,EAAE,MAAM,GAClB,IAAI,CAUN;AAGD,wBAAsB,WAAW,CAC/B,OAAO,GAAE;IACP,YAAY,CAAC,EAAE,OAAO,CAAC;IACvB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,wBAAwB,CAAC,EAAE,OAAO,CAAC;IACnC,2EAA2E;IAC3E,kBAAkB,CAAC,EAAE,MAAM,CAAC;IAC5B,wEAAwE;IACxE,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB;;;OAGG;IACH,gBAAgB,CAAC,EAAE,gBAAgB,CAAC;IACpC,uEAAuE;IACvE,KAAK,CAAC,EAAE,OAAO,CAAC;CACZ,EACN,OAAO,GAAE,kBAAuB,GAC/B,OAAO,CAAC,UAAU,CAAC,CA0pCrB;AAED,OAAO,EAAE,qBAAqB,EAAE,MAAM,qBAAqB,CAAC"}
+{"version":3,"file":"sync.d.ts","sourceRoot":"","sources":["../../src/commands/sync.ts"],"names":[],"mappings":"AA6BA,OAAO,KAAK,EAAE,UAAU,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AA6BjE,OAAO,EAEL,yBAAyB,EAE1B,MAAM,gDAAgD,CAAC;AAGxD,OAAO,EAAE,aAAa,EAAE,MAAM,cAAc,CAAC;AAC7C,OAAO,EACL,KAAK,gBAAgB,EAGtB,MAAM,6BAA6B,CAAC;AAyBrC,OAAO,KAAK,EAAE,4BAA4B,EAAE,MAAM,qBAAqB,CAAC;AA4BxE,qBAAa,SAAU,SAAQ,KAAK;gBACtB,OAAO,EAAE,MAAM;CAI5B;AAmCD,wBAAgB,wBAAwB,CACtC,aAAa,EAAE,MAAM,EACrB,gBAAgB,EAAE,MAAM,EACxB,4BAA4B,UAAQ,EACpC,4BAA4B,GAAE,4BAA4B,EAAO,GAChE,MAAM,EAAE,CAuGV;AAqDD,MAAM,WAAW,UAAW,SAAQ,WAAW;IAC7C,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,UAAU,yBAAyB;IACjC,aAAa,EAAE,MAAM,CAAC;IACtB,QAAQ,EAAE,MAAM,CAAC;IACjB,OAAO,EAAE,OAAO,CAAC;IACjB,WAAW,EAAE,MAAM,CAAC;IACpB,YAAY,EAAE,OAAO,CAAC;CACvB;AAED,UAAU,kBAAkB;IAC1B,WAAW,CAAC,EAAE,CAAC,OAAO,EAAE,yBAAyB,KAAK,OAAO,CAAC,IAAI,CAAC,GAAG,IAAI,CAAC;IAC3E,UAAU,CAAC,EAAE,CACX,OAAO,EAAE,yBAAyB,GAAG;QAAE,UAAU,EAAE,OAAO,CAAA;KAAE,KACzD,OAAO,CAAC,IAAI,CAAC,GAAG,IAAI,CAAC;IAC1B,YAAY,CAAC,EAAE,CAAC,OAAO,EAAE;QAAE,OAAO,EAAE,MAAM,CAAA;KAAE,KAAK,aAAa,CAAC;IAC/D,yBAAyB,CAAC,EAAE,OAAO,yBAAyB,CAAC;CAC9D;AA+FD,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,OAAO,GAAG,IAAI,CAGvE;AAGD,wBAAgB,2BAA2B,CACzC,IAAI,EAAE,MAAM,EACZ,KAAK,EAAE,MAAM,IAAI,GAChB,IAAI,CAMN;AAED,wBAAgB,4BAA4B,CAC1C,WAAW,EAAE,UAAU,EAAE,EACzB,QAAQ,EAAE,OAAO,EACjB,OAAO,EAAE,OAAO,EAChB,aAAa,EAAE,MAAM,EACrB,QAAQ,EAAE,MAAM,GACf,IAAI,CAIN;AAED,wBAAgB,0BAA0B,CAAC,MAAM,EAAE;IACjD,OAAO,EAAE,OAAO,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB,GAAG,IAAI,CAMP;AAED,wBAAgB,iCAAiC,CAC/C,WAAW,EAAE,UAAU,EAAE,EACzB,oBAAoB,EAAE,OAAO,EAC7B,iBAAiB,EAAE,MAAM,EACzB,WAAW,EAAE,MAAM,GAClB,IAAI,CAUN;AAGD,wBAAsB,WAAW,CAC/B,OAAO,GAAE;IACP,YAAY,CAAC,EAAE,OAAO,CAAC;IACvB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,wBAAwB,CAAC,EAAE,OAAO,CAAC;IACnC,2EAA2E;IAC3E,kBAAkB,CAAC,EAAE,MAAM,CAAC;IAC5B,wEAAwE;IACxE,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB;;;OAGG;IACH,gBAAgB,CAAC,EAAE,gBAAgB,CAAC;IACpC,uEAAuE;IACvE,KAAK,CAAC,EAAE,OAAO,CAAC;CACZ,EACN,OAAO,GAAE,kBAAuB,GAC/B,OAAO,CAAC,UAAU,CAAC,CAipCrB;AAED,OAAO,EAAE,qBAAqB,EAAE,MAAM,qBAAqB,CAAC"}

package/dist/commands/sync.js

@@ -36,6 +36,7 @@ import { normalizeExtractionSources, processExtractions, } from "./sync/extracti
 import { refreshManifestCoordinates } from "./sync/manifest.js";
 import { persistEntities, persistRelationships, retractEntitiesById, retractEntitiesForSources, retractEntityRelationshipsById, retractRelationships, } from "./sync/persistence.js";
 import { atomicPublish, atomicPublishGeneration, cleanupStaging, createUniqueStagingPath, prepareStagingEnvironment, } from "./sync/staging.js";
+import { findUntrackedDocumentMatches } from "./sync/untracked-targets.js";
 // Manual deletion of a written-but-unstaged source leaves a recovery receipt
 // behind; sync refuses to guess, so the error must name the way out.
 const PENDING_SOURCE_RECOVERY_HINT = " If the file was deleted on purpose, run 'kibi branch recover --apply' to rebuild the branch KB from the sources that remain.";
@@ -204,6 +205,29 @@ async function checkpointNoopSync(workspaceRoot, branch) {
 function compilerCacheHasEntityDelta(cache) {
     return (cache.entityHashes !== undefined && cache.sourceEntityIds !== undefined);
 }
+/**
+ * Name every dangling relationship and its missing endpoint, and say when an
+ * endpoint is declared in a source sync cannot see (untracked by Git and
+ * without a pending-source receipt): staging that file is the fix.
+ */
+// implements REQ-core-persistence
+function reportDanglingRelationships(workspaceRoot, validationErrors) {
+    console.warn(`Warning: ${validationErrors.length} dangling relationship(s) found`);
+    const missing = new Set();
+    for (const { relationship, error } of validationErrors) {
+        const endpoint = error === "missing_from" ? relationship.from : relationship.to;
+        missing.add(endpoint);
+        console.warn(`  - ${error}: ${relationship.type} ${relationship.from} -> ${relationship.to} (${endpoint} is not in this branch's sources)`);
+    }
+    const untracked = findUntrackedDocumentMatches(workspaceRoot, [...missing]);
+    const byFile = new Map();
+    for (const [id, file] of untracked) {
+        byFile.set(file, [...(byFile.get(file) ?? []), id]);
+    }
+    for (const [file, ids] of byFile) {
+        console.warn(`  Note: ${ids.sort().join(", ")} ${ids.length === 1 ? "is" : "are"} declared in ${file}, which Git does not track and no pending-source receipt covers, so sync ignores it. Run \`git add ${file}\` (staging is enough) or rewrite the entity with kb_upsert, then sync again.`);
+    }
+}
 function compilerCacheIsFresh(cache, workspaceRoot, sourceFiles, nowMs) {
     const sourceKeys = sourceFiles.map((file) => toCacheKey(workspaceRoot, file));
     if (Object.keys(cache.hashes).some((key) => !sourceKeys.includes(key))) {
@@ -852,7 +876,7 @@ export async function syncCommand(options = {}, runtime = {}) {
                     ? []
                     : validateRelationships(allRelationships, entityIds);
                 if (validationErrors.length > 0) {
-                    console.warn(`Warning: ${validationErrors.length} dangling relationship(s) found`);
+                    reportDanglingRelationships(workspaceRoot, validationErrors);
                 }
                 const danglingKeys = new Set(validationErrors.map(({ relationship }) => `${relationship.type}|${relationship.from}|${relationship.to}`));
                 const shardDeltaByKey = new Map();
@@ -973,10 +997,7 @@ export async function syncCommand(options = {}, runtime = {}) {
             const { entityCount, kbModified: entitiesModified } = await persistEntities(prolog, results, entityIds);
             const validationErrors = validateRelationships(allRelationships, entityIds);
             if (validationErrors.length > 0) {
-                console.warn(`Warning: ${validationErrors.length} dangling relationship(s) found`);
-                for (const { relationship, error } of validationErrors) {
-                    console.warn(`  - ${error}: ${relationship.type} ${relationship.from} -> ${relationship.to}`);
-                }
+                reportDanglingRelationships(workspaceRoot, validationErrors);
             }
             const danglingKeys = new Set(validationErrors.map(({ relationship: r }) => `${r.type}|${r.from}|${r.to}`));
             const validRelationships = allRelationships.filter((r) => !danglingKeys.has(`${r.type}|${r.from}|${r.to}`));

package/dist/engine.d.ts

@@ -8,6 +8,10 @@ export { EngineQueryLimitError, QUERY_LIMIT_EXCEEDED_CODE, queryLimitExceededOf,
 export type { EngineLimitExceeded, EngineQueryLimits, } from "./engine-limits.js";
 export declare const ENGINE_PROTOCOL_VERSION = 1;
 export declare const ENGINE_IDLE_TIMEOUT_MS: number;
+/** Upper bound between two wall-clock idle checks of the engine daemon. */
+export declare const ENGINE_IDLE_CHECK_INTERVAL_MS: number;
+/** How long a stopping daemon waits for SWI to halt on stdin EOF. */
+export declare const ENGINE_PROLOG_EXIT_GRACE_MS = 1000;
 /**
  * Package versions this engine build carries (KIBI_PACKAGE_VERSIONS when
  * set). The client sends them on every request and the daemon reports its

package/dist/engine.d.ts.map

@@ -1 +1 @@
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package/dist/engine.js

@@ -34,6 +34,10 @@ const READ_LIMITED_METHODS = new Set([
 ]);
 export const ENGINE_PROTOCOL_VERSION = 1;
 export const ENGINE_IDLE_TIMEOUT_MS = 10 * 60 * 1000;
+/** Upper bound between two wall-clock idle checks of the engine daemon. */
+export const ENGINE_IDLE_CHECK_INTERVAL_MS = 30 * 1000;
+/** How long a stopping daemon waits for SWI to halt on stdin EOF. */
+export const ENGINE_PROLOG_EXIT_GRACE_MS = 1000;
 /**
  * Package versions this engine build carries (KIBI_PACKAGE_VERSIONS when
  * set). The client sends them on every request and the daemon reports its
@@ -1695,7 +1699,12 @@ export async function runEngineDaemon(requestedOptions) {
     writeFileSync(enginePidPath(options.workspaceRoot, options.branch), `${process.pid}\n`, { mode: 0o600 });
     const server = net.createServer();
     let activeClients = 0;
-    let idleTimer = null;
+    // implements REQ-core-journaled-engine-persistence
+    // Idle exit compares wall-clock time: a one-shot timer does not advance
+    // while the host (a VM, a laptop) is suspended, so a daemon would outlive
+    // its idle budget by the whole suspension.
+    let lastActivityAt = Date.now();
+    let idleWatch = null;
     let queue = Promise.resolve();
     let idleCompactionQueued = false;
     const queryCache = new Map();
@@ -1783,12 +1792,17 @@ export async function runEngineDaemon(requestedOptions) {
                 idleCompactionQueued = false;
             });
         }
-        if (idleTimer)
-            clearTimeout(idleTimer);
-        idleTimer = setTimeout(() => {
-            if (activeClients === 0)
+        lastActivityAt = Date.now();
+        if (idleWatch)
+            return;
+        const idleMs = engineIdleTimeoutMs();
+        idleWatch = setInterval(() => {
+            if (!shuttingDown &&
+                activeClients === 0 &&
+                Date.now() - lastActivityAt >= idleMs)
                 void shutdown();
-        }, engineIdleTimeoutMs());
+        }, Math.min(idleMs, ENGINE_IDLE_CHECK_INTERVAL_MS));
+        idleWatch.unref();
     };
     const handle = async (request, cancelledRequests) => {
         if (request.protocolVersion !== ENGINE_PROTOCOL_VERSION) {
@@ -2121,8 +2135,8 @@ export async function runEngineDaemon(requestedOptions) {
         shuttingDown = true;
         process.off("SIGTERM", requestSignalShutdown);
         process.off("SIGINT", requestSignalShutdown);
-        if (idleTimer)
-            clearTimeout(idleTimer);
+        if (idleWatch)
+            clearInterval(idleWatch);
         clearInterval(workspaceWatchdog);
         // Stop accepting clients before the first asynchronous durability step.
         // Keep the PID published until Prolog releases the branch-store lock.
@@ -2131,6 +2145,7 @@ export async function runEngineDaemon(requestedOptions) {
         const saved = session.needsRecycle()
             ? null
             : await prolog.query("kb_save").catch(() => null);
+        let detached = false;
         if (saved?.success) {
             try {
                 fsyncJournaledBranchStore(branchPath);
@@ -2139,8 +2154,22 @@ export async function runEngineDaemon(requestedOptions) {
                 // Shutdown remains best effort. Request-time writes fail closed if
                 // their durability barrier cannot complete.
             }
-        }
-        await prolog.terminate().catch(() => undefined);
+            // implements REQ-core-journaled-engine-persistence
+            // Release the store the way the one-shot path does: kb_detach removes
+            // rdf/lock and the ownership journal. A SIGTERM'd SWI process never
+            // runs its at_halt cleanup, so skipping this left a dead lock behind
+            // on every stop.
+            detached = await prolog
+                .query("kb_detach")
+                .then((result) => result.success)
+                .catch(() => false);
+        }
+        // Once kb_detach released the store, nothing in at_halt is needed and the
+        // child is signalled at once. Otherwise let SWI halt on stdin EOF (running
+        // its at_halt cleanup) for a bounded moment; the wait ends on exit.
+        await prolog
+            .terminate({ graceMs: detached ? 0 : ENGINE_PROLOG_EXIT_GRACE_MS })
+            .catch(() => undefined);
         for (const client of clients)
             client.destroy();
         // A close callback can remain pending on older Node releases when a
@@ -2189,6 +2218,7 @@ export async function runEngineDaemon(requestedOptions) {
                 const bytes = typeof chunk === "string" ? Buffer.from(chunk) : chunk;
                 buffer = parseFrames(Buffer.concat([buffer, bytes]), (value) => {
                     const request = value;
+                    lastActivityAt = Date.now();
                     if (shuttingDown) {
                         writeSocketFrame(socket, {
                             id: request.id,

package/dist/operations/modeling/predicate-applicability.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"predicate-applicability.d.ts","sourceRoot":"","sources":["../../../src/operations/modeling/predicate-applicability.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,KAAK,qBAAqB,EAE3B,MAAM,uBAAuB,CAAC;AAG/B,eAAO,MAAM,uBAAuB,OAAO,CAAC;AAC5C,eAAO,MAAM,0BAA0B,MAAM,CAAC;AAC9C,eAAO,MAAM,qBAAqB,OAAO,CAAC;AA2W1C,MAAM,WAAW,qBAAqB;IACpC,QAAQ,CAAC,QAAQ,EAAE,OAAO,CAAC;IAC3B,QAAQ,CAAC,OAAO,EAAE,SAAS,MAAM,EAAE,CAAC;IACpC,QAAQ,CAAC,kBAAkB,EAAE,MAAM,CAAC;CACrC;AAED;;;;GAIG;AACH,wBAAgB,6BAA6B,CAC3C,MAAM,EAAE,qBAAqB,EAC7B,IAAI,EAAE,MAAM,GACX,qBAAqB,CA2EvB"}
+{"version":3,"file":"predicate-applicability.d.ts","sourceRoot":"","sources":["../../../src/operations/modeling/predicate-applicability.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,KAAK,qBAAqB,EAE3B,MAAM,uBAAuB,CAAC;AAG/B,eAAO,MAAM,uBAAuB,OAAO,CAAC;AAC5C,eAAO,MAAM,0BAA0B,MAAM,CAAC;AAC9C,eAAO,MAAM,qBAAqB,OAAO,CAAC;AA8W1C,MAAM,WAAW,qBAAqB;IACpC,QAAQ,CAAC,QAAQ,EAAE,OAAO,CAAC;IAC3B,QAAQ,CAAC,OAAO,EAAE,SAAS,MAAM,EAAE,CAAC;IACpC,QAAQ,CAAC,kBAAkB,EAAE,MAAM,CAAC;CACrC;AAED;;;;GAIG;AACH,wBAAgB,6BAA6B,CAC3C,MAAM,EAAE,qBAAqB,EAC7B,IAAI,EAAE,MAAM,GACX,qBAAqB,CA2EvB"}

package/dist/operations/modeling/predicate-applicability.js

@@ -2,7 +2,10 @@ import { usageHintsForSchema, } from "./predicate-ranker.js";
 export const MIN_APPLICABILITY_SCORE = 0.62;
 export const STRONG_APPLICABILITY_SCORE = 0.8;
 export const WEAK_CANDIDATE_MARGIN = 0.06;
-const NORMATIVE_OR_VALIDITY_PATTERN = /\b(?:must|shall|should|required|requires?|may\s+only|only\s+.+?\s+(?:may|can)|must\s+not|shall\s+not|cannot|can't|allowed|denied|forbidden|prohibited|invalid|unresolved|reject(?:s|ed|ion)?|fail(?:s|ed|ure)?\s+(?:clearly|explicitly|with)|defaults?\s+to|states?\s+are|owned\s+by|initializes?\s+after|before|unless|when|if|(?:exception|exempt)\s+(?:to|from|when|if|unless))\b/i;
+// A bare permission modal ("coaches can read", "users may export", "are
+// permitted to") states a permission as much as "allowed" does, so it must
+// reach the permission_rule intent rule instead of being rejected here.
+const NORMATIVE_OR_VALIDITY_PATTERN = /\b(?:must|shall|should|required|requires?|may\s+only|only\s+.+?\s+(?:may|can)|(?:can|may)\s+(?:not\s+)?(?:only\s+)?\w+|(?:is|are)\s+(?:not\s+)?(?:allowed|permitted)\s+to|permitted|must\s+not|shall\s+not|cannot|can't|allowed|denied|forbidden|prohibited|invalid|unresolved|reject(?:s|ed|ion)?|fail(?:s|ed|ure)?\s+(?:clearly|explicitly|with)|defaults?\s+to|states?\s+are|owned\s+by|initializes?\s+after|before|unless|when|if|(?:exception|exempt)\s+(?:to|from|when|if|unless))\b/i;
 function expressesNormativeOrValidityIntent(text) {
     return /^\s*no\b/i.test(text) || NORMATIVE_OR_VALIDITY_PATTERN.test(text);
 }
@@ -95,7 +98,7 @@ const INTENT_RULES = {
     },
     permission_rule: {
         allOf: [
-            [/only|may|can|allowed|denied|forbidden|must\s+not|cannot/i],
+            [/only|may|can|allowed|permitted|denied|forbidden|must\s+not|cannot/i],
             [
                 /delete|export|access|read|write|update|remove|manage|permission/i,
                 // A common action verb counts only right after the permission modal

package/dist/operations/modeling/predicate-catalog-4.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"predicate-catalog-4.d.ts","sourceRoot":"","sources":["../../../src/operations/modeling/predicate-catalog-4.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,wBAAwB,EAAE,MAAM,sBAAsB,CAAC;AAGrE,eAAO,MAAM,mBAAmB,EAAE,wBAAwB,EAqTzD,CAAC"}
+{"version":3,"file":"predicate-catalog-4.d.ts","sourceRoot":"","sources":["../../../src/operations/modeling/predicate-catalog-4.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,wBAAwB,EAAE,MAAM,sBAAsB,CAAC;AAGrE,eAAO,MAAM,mBAAmB,EAAE,wBAAwB,EAyTzD,CAAC"}

package/dist/operations/modeling/predicate-catalog-4.js

@@ -203,10 +203,14 @@ export const PREDICATE_CATALOG_4 = [
         argument_names: ["actor", "action", "resource", "decision"],
         argument_types: ["actor", "action", "resource", "decision"],
         ...closedArguments({ decision: DECISION_VOCABULARY }),
+        // One decision per actor, action and resource: an allow and a deny for
+        // the same three contradict (kb.pl builtin_decision_predicate/5).
+        key_arguments: ["actor", "action", "resource"],
         keywords: [
             "may",
             "can",
             "allowed",
+            "permitted",
             "denied",
             "forbidden",
             "must not",

package/dist/operations/modeling/predicate-loader.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"predicate-loader.d.ts","sourceRoot":"","sources":["../../../src/operations/modeling/predicate-loader.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,0CAA0C,CAAC;AAK3E,OAAO,KAAK,EACV,wBAAwB,EACxB,mBAAmB,EACpB,MAAM,sBAAsB,CAAC;AAI9B,wBAAgB,qBAAqB,CAAC,KAAK,EAAE,OAAO,GAAG,MAAM,GAAG,SAAS,CAExE;AAGD,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,wBAAwB,GAAG,IAAI,CACxE,wBAAwB,EACxB,UAAU,CACX,GAAG;IACF,WAAW,EAAE,mBAAmB,CAAC;CAClC,CA4BA;AAGD,wBAAsB,4BAA4B,CAChD,MAAM,EAAE,UAAU,GAAG,IAAI,EACzB,sBAAsB,EAAE,OAAO,EAC/B,QAAQ,EAAE,MAAM,EAAE,GACjB,OAAO,CAAC,wBAAwB,EAAE,CAAC,CAwBrC;AAGD,wBAAgB,yBAAyB,CACvC,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAC9B,wBAAwB,EAAE,CAwD5B;AAGD,wBAAgB,oBAAoB,CAClC,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAC9B,mBAAmB,GAAG,SAAS,CAOjC;AAGD,wBAAgB,WAAW,CAAC,KAAK,EAAE,OAAO,GAAG,MAAM,EAAE,CAQpD"}
+{"version":3,"file":"predicate-loader.d.ts","sourceRoot":"","sources":["../../../src/operations/modeling/predicate-loader.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,0CAA0C,CAAC;AAK3E,OAAO,KAAK,EACV,wBAAwB,EACxB,mBAAmB,EACpB,MAAM,sBAAsB,CAAC;AAI9B,wBAAgB,qBAAqB,CAAC,KAAK,EAAE,OAAO,GAAG,MAAM,GAAG,SAAS,CAExE;AAGD,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,wBAAwB,GAAG,IAAI,CACxE,wBAAwB,EACxB,UAAU,CACX,GAAG;IACF,WAAW,EAAE,mBAAmB,CAAC;CAClC,CA6BA;AAGD,wBAAsB,4BAA4B,CAChD,MAAM,EAAE,UAAU,GAAG,IAAI,EACzB,sBAAsB,EAAE,OAAO,EAC/B,QAAQ,EAAE,MAAM,EAAE,GACjB,OAAO,CAAC,wBAAwB,EAAE,CAAC,CAwBrC;AAGD,wBAAgB,yBAAyB,CACvC,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAC9B,wBAAwB,EAAE,CA0D5B;AAGD,wBAAgB,oBAAoB,CAClC,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAC9B,mBAAmB,GAAG,SAAS,CAOjC;AAGD,wBAAgB,WAAW,CAAC,KAAK,EAAE,OAAO,GAAG,MAAM,EAAE,CAQpD"}

package/dist/operations/modeling/predicate-loader.js

@@ -23,6 +23,7 @@ export function schemaForCandidate(schema) {
         ...(schema.argument_aliases
             ? { argument_aliases: schema.argument_aliases }
             : {}),
+        ...(schema.key_arguments ? { key_arguments: schema.key_arguments } : {}),
         ...(schema.aliases ? { aliases: schema.aliases } : {}),
         ...(schema.paraphrase_templates
             ? { paraphrase_templates: schema.paraphrase_templates }
@@ -64,6 +65,7 @@ export function predicateSchemaFromEntity(entity) {
         return [];
     const usageHints = usageHintsFromEntity(entity);
     const argumentDescriptions = stringArray(entity.argument_descriptions);
+    const keyArguments = stringArray(entity.key_arguments);
     const vocabulary = predicateVocabularyFromEntity(entity);
     return [
         {
@@ -93,6 +95,7 @@ export function predicateSchemaFromEntity(entity) {
                     ])),
                 }
                 : {}),
+            ...(keyArguments.length > 0 ? { key_arguments: keyArguments } : {}),
             keywords: [
                 predicateName,
                 ...stringArray(entity.aliases),

package/dist/operations/modeling/predicate-score-3.js

@@ -51,7 +51,7 @@ export function scoreExactPredicates3(schema, text) {
         return 0;
     }
     if (schema.predicate_name === "permission_rule") {
-        if (/^(?:only\s+)?[a-z][a-z\s_-]*\s+(?:may|can|is\s+allowed\s+to|must\s+not|cannot|can't|is\s+forbidden\s+to)\s+.+?\.?$/i.test(text)) {
+        if (/^(?:only\s+)?[a-z][a-z\s_-]*\s+(?:may|can|(?:is|are)\s+(?:not\s+)?(?:allowed|permitted|forbidden)\s+to|must\s+not|cannot|can't)\s+.+?\.?$/i.test(text)) {
             return 0.98;
         }
         return 0;

package/dist/operations/modeling/predicate-types.d.ts

@@ -16,6 +16,11 @@ export interface PredicateSchemaCandidate {
     argument_constants?: Record<string, string[]>;
     /** Legacy spellings keyed by argument name, each mapped to a constant. */
     argument_aliases?: Record<string, Record<string, string>>;
+    /**
+     * Argument names that determine the remaining arguments (a functional
+     * dependency). Two facts that agree on them describe the same case.
+     */
+    key_arguments?: string[];
     keywords: string[];
     /** Human-language aliases and controlled paraphrase templates used for deterministic retrieval. */
     aliases?: string[];

package/dist/operations/modeling/predicate-types.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"predicate-types.d.ts","sourceRoot":"","sources":["../../../src/operations/modeling/predicate-types.ts"],"names":[],"mappings":"AACA,MAAM,MAAM,iBAAiB,GAAG,QAAQ,GAAG,MAAM,CAAC;AAGlD,MAAM,WAAW,mBAAmB;IAClC,QAAQ,EAAE,MAAM,EAAE,CAAC;IACnB,eAAe,EAAE,MAAM,EAAE,CAAC;CAC3B;AAGD,MAAM,WAAW,wBAAwB;IACvC,EAAE,EAAE,MAAM,CAAC;IACX,cAAc,EAAE,MAAM,CAAC;IACvB,KAAK,EAAE,MAAM,CAAC;IACd,WAAW,EAAE,MAAM,CAAC;IACpB,cAAc,EAAE,MAAM,EAAE,CAAC;IACzB,cAAc,EAAE,MAAM,EAAE,CAAC;IACzB,wEAAwE;IACxE,qBAAqB,CAAC,EAAE,MAAM,EAAE,CAAC;IACjC,qEAAqE;IACrE,kBAAkB,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,CAAC,CAAC;IAC9C,0EAA0E;IAC1E,gBAAgB,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAC;IAC1D;;;OAGG;IACH,aAAa,CAAC,EAAE,MAAM,EAAE,CAAC;IACzB,QAAQ,EAAE,MAAM,EAAE,CAAC;IACnB,mGAAmG;IACnG,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,oBAAoB,CAAC,EAAE,MAAM,EAAE,CAAC;IAChC,QAAQ,EAAE,MAAM,EAAE,CAAC;IACnB,IAAI,EAAE,MAAM,EAAE,CAAC;IACf,WAAW,CAAC,EAAE,mBAAmB,CAAC;CACnC;AAGD,MAAM,MAAM,qBAAqB,GAAG,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,GAAG;IACtE,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;IACtB,QAAQ,CAAC,aAAa,CAAC,EAAE,MAAM,CAAC;IAChC,QAAQ,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACzB,QAAQ,CAAC,WAAW,CAAC,EAAE,MAAM,CAAC;IAC9B,QAAQ,CAAC,aAAa,CAAC,EAAE,MAAM,CAAC;IAChC,QAAQ,CAAC,QAAQ,CAAC,EAAE,MAAM,CAAC;IAC3B,QAAQ,CAAC,sBAAsB,CAAC,EAAE,OAAO,CAAC;IAC1C,+EAA+E;IAC/E,QAAQ,CAAC,QAAQ,CAAC,EAAE,MAAM,CAAC;IAC3B,4EAA4E;IAC5E,QAAQ,CAAC,gBAAgB,CAAC,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAC;IAC7D,qEAAqE;IACrE,QAAQ,CAAC,YAAY,CAAC,EAAE,iBAAiB,CAAC;IAC1C,mFAAmF;IACnF,QAAQ,CAAC,mBAAmB,CAAC,EAAE,SAAS,MAAM,EAAE,CAAC;CAClD,CAAC;AAGF,MAAM,WAAW,mBAAmB;IAClC,EAAE,EAAE,MAAM,CAAC;IACX,cAAc,EAAE,MAAM,CAAC;IACvB,cAAc,EAAE,MAAM,EAAE,CAAC;IACzB,aAAa,EAAE,MAAM,CAAC;IACtB,QAAQ,EAAE,iBAAiB,CAAC;IAC5B,cAAc,EAAE,UAAU,GAAG,YAAY,CAAC;IAC1C,iBAAiB,EAAE,MAAM,EAAE,CAAC;IAC5B,+EAA+E;IAC/E,kBAAkB,EAAE,iBAAiB,CAAC;IACtC,iFAAiF;IACjF,8BAA8B,EAAE,MAAM,CAAC,MAAM,EAAE,iBAAiB,CAAC,CAAC;IAClE;;;;OAIG;IACH,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B;;;;OAIG;IACH,eAAe,EAAE,QAAQ,GAAG,UAAU,GAAG,cAAc,CAAC;IACxD,WAAW,EAAE,UAAU,GAAG,UAAU,CAAC;IACrC,iBAAiB,EAAE,MAAM,EAAE,CAAC;IAC5B,mBAAmB,EAAE,MAAM,CAAC;IAC5B,gBAAgB,EAAE,wBAAwB,CAAC;IAC3C,KAAK,EAAE,MAAM,CAAC;IACd,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,EAAE,IAAI,CAAC,wBAAwB,EAAE,UAAU,CAAC,GAAG;QACnD,WAAW,EAAE,mBAAmB,CAAC;KAClC,CAAC;CACH;AAED,MAAM,MAAM,iBAAiB,GACzB,UAAU,GACV,aAAa,GACb,WAAW,GACX,UAAU,GACV,aAAa,CAAC;AAElB,MAAM,WAAW,wBAAwB;IACvC,aAAa,EAAE,MAAM,CAAC;IACtB,YAAY,EAAE,MAAM,CAAC;IACrB,kBAAkB,EAAE,MAAM,CAAC;IAC3B,WAAW,EAAE,MAAM,CAAC;IACpB,iBAAiB,EAAE,MAAM,CAAC;IAC1B,mBAAmB,EAAE,MAAM,CAAC;IAC5B,iBAAiB,EAAE,MAAM,CAAC;IAC1B,KAAK,EAAE,MAAM,CAAC;CACf;AAED,MAAM,WAAW,0BAA0B;IACzC,cAAc,EAAE,MAAM,CAAC;IACvB,KAAK,EAAE,MAAM,CAAC;IACd,WAAW,EAAE,MAAM,CAAC;IACpB,cAAc,EAAE,MAAM,EAAE,CAAC;IACzB,cAAc,EAAE,MAAM,EAAE,CAAC;IACzB,qBAAqB,CAAC,EAAE,MAAM,EAAE,CAAC;IACjC,kBAAkB,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAC3C,mBAAmB,EAAE,MAAM,EAAE,CAAC;IAC9B,SAAS,EAAE,MAAM,CAAC;IAClB,WAAW,EAAE,MAAM,CAAC;CACrB;AAED;;;;GAIG;AAEH,MAAM,WAAW,WAAW;IAC1B,QAAQ,EAAE,MAAM,CAAC;IACjB,QAAQ,EAAE,MAAM,CAAC;IACjB,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,aAAa,CAAC,EAAE,MAAM,EAAE,CAAC;IACzB,QAAQ,EAAE,MAAM,EAAE,CAAC;IACnB,YAAY,EAAE,MAAM,CAAC;IACrB,UAAU,EAAE,iBAAiB,CAAC;IAC9B,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,gFAAgF;AAEhF,MAAM,WAAW,sBAAsB;IACrC,YAAY,EAAE;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAC;QAAC,EAAE,EAAE,MAAM,CAAA;KAAE,CAAC;IACzD,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,MAAM,GAAG,IAAI,CAAC;IACxB,QAAQ,EAAE,MAAM,CAAC;CAClB;AAGD,MAAM,WAAW,uBAAuB;IACtC,OAAO,EAAE,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IAC/C,iBAAiB,EAAE;QACjB,IAAI,EAAE,MAAM,CAAC;QACb,QAAQ,EAAE,MAAM,CAAC;QACjB,WAAW,EAAE,MAAM,EAAE,CAAC;QACtB,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;QACtB,aAAa,EAAE,MAAM,GAAG,IAAI,CAAC;QAC7B,OAAO,EAAE,MAAM,CAAC;QAChB,UAAU,EAAE,mBAAmB,EAAE,CAAC;QAClC,iBAAiB,EACb,0BAA0B,GAC1B,2BAA2B,GAC3B,0BAA0B,GAC1B,qBAAqB,GACrB,mBAAmB,GACnB,mBAAmB,CAAC;QACxB,0BAA0B,EAAE,0BAA0B,GAAG,IAAI,CAAC;QAC9D,SAAS,EAAE,KAAK,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC;QAC1C,gBAAgB,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC;QACjD,kGAAkG;QAClG,kBAAkB,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;QACnC,iBAAiB,CAAC,EAAE,sBAAsB,EAAE,CAAC;QAC7C,eAAe,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC;QACjD,gGAAgG;QAChG,YAAY,CAAC,EAAE,WAAW,EAAE,CAAC;QAC7B,QAAQ,EAAE,MAAM,EAAE,CAAC;KACpB,CAAC;IACF,SAAS,EAAE,KAAK,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC;CAC3C"}

package/dist/operations/mutation/source-authoring.d.ts

@@ -80,6 +80,15 @@ export declare function renderYamlRelationshipDeletion(sourcePathValue: string,
  * so a plan writes exactly what `kb_upsert` would.
  */
 export declare function renderSourceDocument(input: UpsertInput, entity: Readonly<Record<string, unknown>>, existingContent: string | undefined, relativePath: string): string;
+/**
+ * Whether Git definitely does not track `relative`. Sync reads only tracked
+ * sources plus pending-source receipts, so an untracked file (for example the
+ * `.kb/symbols.yaml` that `kibi init` creates) needs a receipt on every
+ * write, or a new branch store compiles relationships without the entities
+ * they connect. Any other Git outcome (not a repository, git missing) is
+ * "unknown" and keeps the previous behaviour.
+ */
+export declare function isUntrackedByGit(workspaceRoot: string, relative: string): boolean;
 export declare function writeSourceForUpsert(input: UpsertInput, entity: Readonly<Record<string, unknown>>, existing?: Readonly<Record<string, unknown>>, context?: OperationContext, sourceDocumentOverride?: string): Promise<{
     receipt: SourceWriteReceipt;
     rollback: () => Promise<void>;

package/dist/operations/mutation/source-authoring.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"source-authoring.d.ts","sourceRoot":"","sources":["../../../src/operations/mutation/source-authoring.ts"],"names":[],"mappings":"AAUA,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,0CAA0C,CAAC;AAMjF,OAAO,KAAK,EAAqB,WAAW,EAAE,MAAM,YAAY,CAAC;AAEjE,MAAM,MAAM,kBAAkB,GAAG,QAAQ,CAAC;IACxC,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,OAAO,GAAG,QAAQ,CAAC;IACzB,UAAU,EAAE,MAAM,GAAG,IAAI,CAAC;IAC1B,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,OAAO,EAAE,OAAO,CAAC;CAClB,CAAC,CAAC;AAmBH,wBAAgB,yBAAyB,CACvC,aAAa,EAAE,MAAM,EACrB,YAAY,EAAE,MAAM,EACpB,SAAS,EAAE,MAAM,GAChB,IAAI,CAiBN;AAED,KAAK,SAAS,GAAG,QAAQ,CAAC;IAAE,KAAK,EAAE,IAAI,CAAC;IAAC,KAAK,EAAE,IAAI,CAAA;CAAE,CAAC,CAAC;AAExD,8EAA8E;AAE9E,wBAAgB,aAAa,CAAC,YAAY,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI,CAOpE;AAED;;;;GAIG;AAEH,wBAAgB,gBAAgB,CAC9B,YAAY,EAAE,MAAM,EACpB,KAAK,EAAE,SAAS,GAAG,IAAI,GACtB,IAAI,CAON;AAeD;;;;GAIG;AAEH,wBAAgB,0BAA0B,CACxC,aAAa,EAAE,MAAM,EACrB,YAAY,EAAE,MAAM,GACnB,IAAI,CAMN;AAgBD,wBAAgB,0BAA0B,CACxC,aAAa,EAAE,MAAM,EACrB,QAAQ,EAAE,MAAM,GACf,MAAM,CAqCR;AAED,wBAAgB,2BAA2B,CACzC,aAAa,EAAE,MAAM,EACrB,MAAM,EAAE,MAAM,GACb,MAAM,CAoBR;AAsBD;;;;GAIG;AACH,wBAAgB,sBAAsB,CACpC,aAAa,EAAE,MAAM,EACrB,IAAI,EAAE,MAAM,GACX,MAAM,GAAG,SAAS,CAYpB;AAED,wBAAgB,yBAAyB,CACvC,aAAa,EAAE,MAAM,EACrB,IAAI,EAAE,MAAM,GACX,OAAO,CAET;AAkGD,uFAAuF;AAEvF,eAAO,MAAM,uBAAuB,uGAM1B,CAAC;AA8BX,wBAAgB,qBAAqB,CACnC,IAAI,EAAE,OAAO,GACZ,KAAK,CAAC;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,CAAC,CAiCzC;AAgSD,wBAAgB,oBAAoB,CAClC,eAAe,EAAE,MAAM,EACvB,QAAQ,EAAE,MAAM,EAChB,UAAU,EAAE,MAAM,EAClB,eAAe,EAAE,MAAM,GACtB;IAAE,IAAI,EAAE,OAAO,GAAG,QAAQ,CAAC;IAAC,IAAI,CAAC,EAAE,MAAM,CAAA;CAAE,CA6C7C;AAED;;;;;;;GAOG;AACH,wBAAgB,kCAAkC,CAChD,eAAe,EAAE,MAAM,EACvB,eAAe,EAAE,MAAM,EACvB,QAAQ,EAAE,QAAQ,CAAC;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAC;IAAC,EAAE,EAAE,MAAM,CAAA;CAAE,CAAC,GAC7D;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,OAAO,CAAA;CAAE,CA4DpC;AAED;;;;GAIG;AACH,wBAAgB,8BAA8B,CAC5C,eAAe,EAAE,MAAM,EACvB,eAAe,EAAE,MAAM,EACvB,QAAQ,EAAE,QAAQ,CAAC;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAC;IAAC,EAAE,EAAE,MAAM,CAAA;CAAE,CAAC,GAC7D;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,OAAO,CAAA;CAAE,CAiEpC;AAED;;;;GAIG;AAEH,wBAAgB,oBAAoB,CAClC,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,EACzC,eAAe,EAAE,MAAM,GAAG,SAAS,EACnC,YAAY,EAAE,MAAM,GACnB,MAAM,CAsBR;AAED;;;;;;;GAOG;AAEH,wBAAgB,gBAAgB,CAC9B,aAAa,EAAE,MAAM,EACrB,QAAQ,EAAE,MAAM,GACf,OAAO,CAaT;AAED,wBAAsB,oBAAoB,CACxC,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,EACzC,QAAQ,CAAC,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,EAC5C,OAAO,CAAC,EAAE,gBAAgB,EAC1B,sBAAsB,CAAC,EAAE,MAAM,GAC9B,OAAO,CAAC;IACT,OAAO,EAAE,kBAAkB,CAAC;IAC5B,QAAQ,EAAE,MAAM,OAAO,CAAC,IAAI,CAAC,CAAC;CAC/B,GAAG,IAAI,CAAC,CA+IR;AAED,uEAAuE;AACvE,wBAAgB,mBAAmB,CACjC,OAAO,EAAE,gBAAgB,EACzB,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,EACzC,QAAQ,CAAC,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,GAC3C,MAAM,CAOR"}

package/dist/operations/mutation/source-authoring.js

@@ -1,3 +1,4 @@
+import { execFileSync } from "node:child_process";
 import { createHash } from "node:crypto";
 import { randomUUID } from "node:crypto";
 import fs from "node:fs";
@@ -462,7 +463,19 @@ function renderSymbolManifest(entity, relationships, existingContent) {
     if (!symbols || typeof symbols !== "object" || !("items" in symbols)) {
         throw new OperationError("SOURCE_FORMAT_INVALID", "Symbol manifest must contain a symbols array");
     }
-    const items = symbols.items;
+    // implements REQ-core-persistence
+    // `kibi init` writes `symbols: []`, a flow sequence; appending to it kept
+    // every symbol on one line. Render the list (and the entries that were
+    // written inside it) as block YAML so diffs stay reviewable.
+    const sequence = symbols;
+    if (sequence.flow === true) {
+        sequence.flow = false;
+        for (const item of sequence.items) {
+            if (item && typeof item === "object" && "flow" in item)
+                item.flow = false;
+        }
+    }
+    const items = sequence.items;
     const id = String(entity.id);
     const indices = items.flatMap((item, index) => {
         if (!item || typeof item !== "object" || !("get" in item))
@@ -670,6 +683,27 @@ export function renderSourceDocument(input, entity, existingContent, relativePat
     }
     return renderEntityDocument(input, entity, existingContent);
 }
+/**
+ * Whether Git definitely does not track `relative`. Sync reads only tracked
+ * sources plus pending-source receipts, so an untracked file (for example the
+ * `.kb/symbols.yaml` that `kibi init` creates) needs a receipt on every
+ * write, or a new branch store compiles relationships without the entities
+ * they connect. Any other Git outcome (not a repository, git missing) is
+ * "unknown" and keeps the previous behaviour.
+ */
+// implements REQ-core-persistence
+export function isUntrackedByGit(workspaceRoot, relative) {
+    try {
+        execFileSync("git", ["-C", workspaceRoot, "ls-files", "--error-unmatch", "--", relative], 
+        // Bounded: a write must never wait on Git. A timeout reads as
+        // "tracked", the pre-receipt behaviour.
+        { stdio: "ignore", timeout: 10_000 });
+        return false;
+    }
+    catch (error) {
+        return error.status === 1;
+    }
+}
 export async function writeSourceForUpsert(input, entity, existing, context, sourceDocumentOverride) {
     if (!context?.fs)
         return null;
@@ -795,7 +829,9 @@ export async function writeSourceForUpsert(input, entity, existing, context, sou
     };
     try {
         if (receipt.afterHash !== null &&
-            (before === undefined || fs.existsSync(pendingReceipt))) {
+            (before === undefined ||
+                fs.existsSync(pendingReceipt) ||
+                isUntrackedByGit(context.workspaceRoot, relative))) {
             writePendingSourceReceipt(context.workspaceRoot, relative, receipt.afterHash);
         }
     }

package/dist/operations/planning/apply-plan.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"apply-plan.d.ts","sourceRoot":"","sources":["../../../src/operations/planning/apply-plan.ts"],"names":[],"mappings":"AAyBA,OAAO,KAAK,EAEV,gBAAgB,EAGjB,MAAM,0CAA0C,CAAC;AASlD,OAAO,EACL,KAAK,eAAe,EAIrB,MAAM,uBAAuB,CAAC;AAgE/B,OAAO,KAAK,EACV,aAAa,EACb,eAAe,EAGhB,MAAM,uBAAuB,CAAC;AAE/B,YAAY,EACV,aAAa,EACb,eAAe,EACf,kBAAkB,GACnB,MAAM,uBAAuB,CAAC;AAG/B,eAAO,MAAM,yBAAyB,EAAG,2BAAoC,CAAC;AA6G9E,wBAAgB,iCAAiC,CAC/C,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,EAChB,SAAS,EAAE,MAAM,GAChB,IAAI,CAMN;AAED,wBAAgB,mCAAmC,CACjD,SAAS,EAAE,SAAS;IAAE,EAAE,EAAE,MAAM,CAAC;IAAC,SAAS,CAAC,EAAE,SAAS,MAAM,EAAE,CAAA;CAAE,EAAE,EACnE,OAAO,EAAE,WAAW,CAAC,MAAM,CAAC,GAC3B,IAAI,CAaN;AAED,wBAAgB,qBAAqB,CACnC,OAAO,EAAE,SAAS,eAAe,EAAE,EACnC,SAAS,cAAoB,GAC5B,eAAe,EAAE,CA2CnB;AA8zBD;;;;;;GAMG;AAEH,wBAAsB,kBAAkB,CACtC,IAAI,EAAE,aAAa,EACnB,OAAO,EAAE,gBAAgB,GACxB,OAAO,CAAC,IAAI,CAAC,CAiCf;AAyqDD,wBAAsB,gBAAgB,CACpC,IAAI,EAAE,aAAa,EACnB,OAAO,EAAE,gBAAgB,GACxB,OAAO,CAAC;IACT,OAAO,EAAE,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IAC/C,iBAAiB,EAAE,eAAe,CAAC;CACpC,CAAC,CAkDD"}

package/dist/operations/planning/apply-plan.js

@@ -7,7 +7,7 @@ import { syncCommand } from "../../commands/sync.js";
 import { PROOF_INTEGRATION_CONFIGURE, applyProofIntegrationAction, } from "../../proof/integration-plan.js";
 import { loadEntities } from "../../public/operations/discovery-entities.js";
 import { executeStatus } from "../../public/operations/discovery-executors.js";
-import { PREDICATE_SCHEMA_ALIGNMENT_CODE, migrationPlanHash, } from "../../public/operations/migration-plan.js";
+import { FRESHNESS_RESYNC, PREDICATE_SCHEMA_ALIGNMENT_CODE, migrationPlanHash, } from "../../public/operations/migration-plan.js";
 import { readMigrationConfigStatus } from "../../public/operations/migration-plan.js";
 import { readWorkspaceSnapshot } from "../../public/operations/workspace-snapshot.js";
 import { computeShardPath, renderShardWithRelationship, } from "../../relationships/shards.js";
@@ -2305,6 +2305,15 @@ async function applyMigrationAction(action, context) {
                 throw new Error("Compiling the branch store (kibi sync) did not complete successfully.");
             return;
         }
+        // implements REQ-cli-status-pre-first-sync
+        case FRESHNESS_RESYNC: {
+            const result = await syncCommand({
+                workspaceRoot: context.workspaceRoot,
+            });
+            if (!result.success)
+                throw new Error("Recompiling changed sources (kibi sync) did not complete successfully.");
+            return;
+        }
         case "damaged_exact_branch_store":
             await branchRecoverCommand({
                 apply: true,

package/dist/operations/semantic-advisor/clauses.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"clauses.d.ts","sourceRoot":"","sources":["../../../src/operations/semantic-advisor/clauses.ts"],"names":[],"mappings":"AAEA,MAAM,MAAM,cAAc,GAAG,QAAQ,CAAC;IACpC,SAAS,EAAE,MAAM,CAAC;IAClB,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,SAAS,EAAE,OAAO,CAAC;IACnB,MAAM,EAAE,UAAU,GAAG,UAAU,CAAC;CACjC,CAAC,CAAC;AAYH,wBAAgB,qBAAqB,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAE3D;AAQD,wBAAgB,gBAAgB,CAC9B,IAAI,EAAE,MAAM,EACZ,QAAQ,CAAC,EAAE,MAAM,GAChB,WAAW,GAAG,aAAa,CAG7B;AAED,wBAAgB,uBAAuB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAW7D;AAED,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAIrD;AA4BD,wBAAgB,sBAAsB,CACpC,IAAI,EAAE,MAAM,EACZ,eAAe,CAAC,EAAE,SAAS,MAAM,EAAE,GAClC,SAAS,cAAc,EAAE,CA4B3B"}
+{"version":3,"file":"clauses.d.ts","sourceRoot":"","sources":["../../../src/operations/semantic-advisor/clauses.ts"],"names":[],"mappings":"AAEA,MAAM,MAAM,cAAc,GAAG,QAAQ,CAAC;IACpC,SAAS,EAAE,MAAM,CAAC;IAClB,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,SAAS,EAAE,OAAO,CAAC;IACnB,MAAM,EAAE,UAAU,GAAG,UAAU,CAAC;CACjC,CAAC,CAAC;AAkBH,wBAAgB,qBAAqB,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAE3D;AAQD,wBAAgB,gBAAgB,CAC9B,IAAI,EAAE,MAAM,EACZ,QAAQ,CAAC,EAAE,MAAM,GAChB,WAAW,GAAG,aAAa,CAG7B;AAED,wBAAgB,uBAAuB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAW7D;AAED,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAIrD;AA4BD,wBAAgB,sBAAsB,CACpC,IAAI,EAAE,MAAM,EACZ,eAAe,CAAC,EAAE,SAAS,MAAM,EAAE,GAClC,SAAS,cAAc,EAAE,CA4B3B"}