@cleocode/cleo 2026.4.39 → 2026.4.41

package/dist/cli/commands/self-update.js

@@ -317,6 +317,40 @@ async function runPostUpdateDiagnostics(opts) {
         }
     }
     else {
+        // No storage migration needed, but still run structural upgrade to ensure
+        // all databases (brain.db, signaldock.db, conduit.db), adapters, schemas,
+        // memory-bridge.md, and other scaffold items are up to date.
+        if (!opts?.skipUpgrade) {
+            const result = await runUpgrade({ autoMigrate: false });
+            if (result.applied > 0 || result.errors.length > 0) {
+                // Show structured output of each action taken
+                if (result.actions.length > 0) {
+                    process.stderr.write('Post-update maintenance:\n');
+                    for (const action of result.actions) {
+                        if (action.status === 'skipped')
+                            continue;
+                        const icon = action.status === 'applied' ? '  ✓' : action.status === 'error' ? '  ✗' : '  -';
+                        process.stderr.write(`${icon} ${action.action}: ${action.details}\n`);
+                    }
+                    process.stderr.write('\n');
+                }
+                cliOutput({
+                    postUpdate: true,
+                    upgrade: {
+                        success: result.success,
+                        applied: result.applied,
+                        actions: result.actions,
+                        errors: result.errors.length > 0 ? result.errors : undefined,
+                    },
+                }, {
+                    command: 'self-update',
+                    message: result.success
+                        ? `Post-update maintenance complete (${result.applied} action(s) applied).`
+                        : 'Post-update maintenance had errors.',
+                });
+                return;
+            }
+        }
         cliOutput({
             postUpdate: true,
             storagePreflight: {

package/dist/cli/commands/self-update.js.map

@@ -1 +1 @@
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package/dist/cli/index.js

@@ -85616,6 +85616,7 @@ var init_error_registry = __esm({
 // packages/core/src/init.ts
 var init_exports = {};
 __export(init_exports, {
+  deployStarterBundle: () => deployStarterBundle,
   ensureInitialized: () => ensureInitialized,
   getVersion: () => getVersion2,
   initAgentDefinition: () => initAgentDefinition,
@@ -86101,53 +86102,7 @@ async function initProject(opts = {}) {
     );
   }
   try {
-    const cantDir = join106(cleoDir, "cant");
-    const cantAgentsDir = join106(cantDir, "agents");
-    const hasCantFiles = existsSync107(cantDir) && readdirSync36(cantDir, { recursive: true }).some(
-      (f2) => typeof f2 === "string" && f2.endsWith(".cant")
-    );
-    if (!hasCantFiles) {
-      let starterBundleSrc = null;
-      try {
-        const { createRequire: createRequire19 } = await import("node:module");
-        const req = createRequire19(import.meta.url);
-        const cleoOsPkgMain = req.resolve("@cleocode/cleo-os/package.json");
-        const cleoOsPkgRoot = dirname22(cleoOsPkgMain);
-        const candidate = join106(cleoOsPkgRoot, "starter-bundle");
-        if (existsSync107(candidate)) {
-          starterBundleSrc = candidate;
-        }
-      } catch {
-      }
-      if (!starterBundleSrc) {
-        const packageRoot = getPackageRoot();
-        const fallbacks = [
-          join106(packageRoot, "..", "cleo-os", "starter-bundle"),
-          join106(packageRoot, "..", "..", "packages", "cleo-os", "starter-bundle")
-        ];
-        starterBundleSrc = fallbacks.find((p2) => existsSync107(p2)) ?? null;
-      }
-      if (starterBundleSrc) {
-        await mkdir16(cantDir, { recursive: true });
-        await mkdir16(cantAgentsDir, { recursive: true });
-        const teamSrc = join106(starterBundleSrc, "team.cant");
-        const teamDst = join106(cantDir, "team.cant");
-        if (existsSync107(teamSrc) && !existsSync107(teamDst)) {
-          await copyFile4(teamSrc, teamDst);
-        }
-        const agentsSrc = join106(starterBundleSrc, "agents");
-        if (existsSync107(agentsSrc)) {
-          const agentFiles = readdirSync36(agentsSrc).filter((f2) => f2.endsWith(".cant"));
-          for (const agentFile of agentFiles) {
-            const dst = join106(cantAgentsDir, agentFile);
-            if (!existsSync107(dst)) {
-              await copyFile4(join106(agentsSrc, agentFile), dst);
-            }
-          }
-        }
-        created.push("starter-bundle: team + agent .cant files deployed to .cleo/cant/");
-      }
-    }
+    await deployStarterBundle(cleoDir, created, warnings);
   } catch (err) {
     warnings.push(`Starter bundle deploy: ${err instanceof Error ? err.message : String(err)}`);
   }
@@ -86275,6 +86230,58 @@ async function getVersion2(projectRoot) {
   }
   return { version: "0.0.0" };
 }
+async function deployStarterBundle(cleoDir, created, warnings) {
+  const cantDir = join106(cleoDir, "cant");
+  const cantAgentsDir = join106(cantDir, "agents");
+  const hasCantFiles = existsSync107(cantDir) && readdirSync36(cantDir, { recursive: true }).some(
+    (f2) => typeof f2 === "string" && f2.endsWith(".cant")
+  );
+  if (hasCantFiles) return;
+  let starterBundleSrc = null;
+  try {
+    const { createRequire: createRequire19 } = await import("node:module");
+    const req = createRequire19(import.meta.url);
+    const cleoOsPkgMain = req.resolve("@cleocode/cleo-os/package.json");
+    const cleoOsPkgRoot = dirname22(cleoOsPkgMain);
+    const candidate = join106(cleoOsPkgRoot, "starter-bundle");
+    if (existsSync107(candidate)) {
+      starterBundleSrc = candidate;
+    }
+  } catch {
+  }
+  if (!starterBundleSrc) {
+    const packageRoot = getPackageRoot();
+    const fallbacks = [
+      join106(packageRoot, "..", "cleo-os", "starter-bundle"),
+      join106(packageRoot, "..", "..", "packages", "cleo-os", "starter-bundle")
+    ];
+    starterBundleSrc = fallbacks.find((p2) => existsSync107(p2)) ?? null;
+  }
+  if (!starterBundleSrc) {
+    warnings.push(
+      "Starter bundle not found \u2014 .cleo/cant/ will remain empty. Run cleo init in a project with @cleocode/cleo-os installed."
+    );
+    return;
+  }
+  await mkdir16(cantDir, { recursive: true });
+  await mkdir16(cantAgentsDir, { recursive: true });
+  const teamSrc = join106(starterBundleSrc, "team.cant");
+  const teamDst = join106(cantDir, "team.cant");
+  if (existsSync107(teamSrc) && !existsSync107(teamDst)) {
+    await copyFile4(teamSrc, teamDst);
+  }
+  const agentsSrc = join106(starterBundleSrc, "agents");
+  if (existsSync107(agentsSrc)) {
+    const agentFiles = readdirSync36(agentsSrc).filter((f2) => f2.endsWith(".cant"));
+    for (const agentFile of agentFiles) {
+      const dst = join106(cantAgentsDir, agentFile);
+      if (!existsSync107(dst)) {
+        await copyFile4(join106(agentsSrc, agentFile), dst);
+      }
+    }
+  }
+  created.push("starter-bundle: team + agent .cant files deployed to .cleo/cant/");
+}
 var DIR_SYMLINK_TYPE2;
 var init_init = __esm({
   "packages/core/src/init.ts"() {
@@ -100127,6 +100134,18 @@ async function runUpgrade(options = {}) {
       });
     } catch {
     }
+    try {
+      const { ensureConduitDb: ensureConduitDb2 } = await Promise.resolve().then(() => (init_conduit_sqlite(), conduit_sqlite_exports));
+      const cdResult = ensureConduitDb2(projectRootForMaint);
+      if (cdResult.action === "created") {
+        actions.push({
+          action: "ensure_conduit_db",
+          status: "applied",
+          details: "conduit.db created with full schema"
+        });
+      }
+    } catch {
+    }
     try {
       const { writeMemoryBridge: writeMemoryBridge2 } = await Promise.resolve().then(() => (init_memory_bridge(), memory_bridge_exports));
       const bridgeResult = await writeMemoryBridge2(projectRootForMaint);
@@ -100163,6 +100182,27 @@ async function runUpgrade(options = {}) {
       }
     } catch {
     }
+    try {
+      const { deployStarterBundle: deployStarterBundle2 } = await Promise.resolve().then(() => (init_init(), init_exports));
+      const cantCreated = [];
+      const cantWarnings = [];
+      await deployStarterBundle2(cleoDir, cantCreated, cantWarnings);
+      if (cantCreated.length > 0) {
+        actions.push({
+          action: "cant_starter_bundle",
+          status: "applied",
+          details: cantCreated.join(", ")
+        });
+      }
+      for (const w2 of cantWarnings) {
+        actions.push({
+          action: "cant_starter_bundle",
+          status: "skipped",
+          details: w2
+        });
+      }
+    } catch {
+    }
     try {
       const skillsCreated = [];
       const skillsWarnings = [];
@@ -100239,6 +100279,43 @@ async function runUpgrade(options = {}) {
       }
     } catch {
     }
+    try {
+      const { AdapterManager: AdapterManager2 } = await Promise.resolve().then(() => (init_adapters(), adapters_exports));
+      const mgr = AdapterManager2.getInstance(projectRootForMaint);
+      const manifests = mgr.discover();
+      if (manifests.length > 0) {
+        const detected = mgr.detectActive();
+        for (const adapterId of detected) {
+          try {
+            const adapter = await mgr.activate(adapterId);
+            const installResult = await adapter.install.install({
+              projectDir: projectRootForMaint
+            });
+            if (installResult.success) {
+              actions.push({
+                action: "adapter_install",
+                status: "applied",
+                details: `Adapter ${adapterId}: installed/updated`
+              });
+            }
+          } catch {
+          }
+        }
+      }
+    } catch {
+    }
+    try {
+      const { ensureCleoOsHub: ensureCleoOsHub2 } = await Promise.resolve().then(() => (init_scaffold(), scaffold_exports));
+      const hubResult = await ensureCleoOsHub2();
+      if (hubResult.action === "created") {
+        actions.push({
+          action: "cleoos_hub",
+          status: "applied",
+          details: hubResult.details ?? "CleoOS hub scaffolded"
+        });
+      }
+    } catch {
+    }
   } else {
     const { existsSync: fsExistsSync } = await import("node:fs");
     const { join: pathJoin } = await import("node:path");
@@ -100445,6 +100522,57 @@ async function diagnoseUpgrade(options = {}) {
             fix: "Run: cleo upgrade"
           });
         }
+        const brainColumnChecks = [
+          {
+            table: "brain_page_nodes",
+            columns: ["quality_score", "content_hash", "last_activity_at", "updated_at"],
+            task: "T528"
+          },
+          {
+            table: "brain_decisions",
+            columns: [
+              "quality_score",
+              "memory_tier",
+              "memory_type",
+              "verified",
+              "valid_at",
+              "invalid_at",
+              "source_confidence",
+              "citation_count"
+            ],
+            task: "T531/T549"
+          },
+          {
+            table: "brain_observations",
+            columns: ["quality_score", "memory_tier", "memory_type", "verified"],
+            task: "T531/T549"
+          }
+        ];
+        const allBrainColsMissing = [];
+        for (const { table, columns, task } of brainColumnChecks) {
+          const hasTable = nativeDb.prepare("SELECT name FROM sqlite_master WHERE type='table' AND name=?").get(table);
+          if (!hasTable?.name) continue;
+          const cols = nativeDb.prepare(`PRAGMA table_info(${table})`).all();
+          const colNames = new Set(cols.map((c) => c.name));
+          const missing = columns.filter((c) => !colNames.has(c));
+          if (missing.length > 0) {
+            allBrainColsMissing.push(`${table}: ${missing.join(", ")} (${task})`);
+          }
+        }
+        if (allBrainColsMissing.length > 0) {
+          findings.push({
+            check: "brain.db.schema_columns",
+            status: "error",
+            details: `Missing brain schema columns: ${allBrainColsMissing.join("; ")}`,
+            fix: "Run: cleo upgrade (will add missing columns automatically)"
+          });
+        } else {
+          findings.push({
+            check: "brain.db.schema_columns",
+            status: "ok",
+            details: "All T528/T531/T549 brain schema columns present"
+          });
+        }
       } else {
         findings.push({
           check: "brain.db.connection",
@@ -100463,7 +100591,80 @@ async function diagnoseUpgrade(options = {}) {
     findings.push({
       check: "brain.db",
       status: "warning",
-      details: "brain.db not found (will be created on first use)"
+      details: "brain.db not found (will be created on first use)",
+      fix: "Run: cleo upgrade"
+    });
+  }
+  const signaldockDbPath = join115(cleoDir, "signaldock.db");
+  if (existsSync118(signaldockDbPath)) {
+    findings.push({
+      check: "signaldock.db",
+      status: "ok",
+      details: "signaldock.db exists"
+    });
+  } else {
+    findings.push({
+      check: "signaldock.db",
+      status: "warning",
+      details: "signaldock.db not found",
+      fix: "Run: cleo upgrade"
+    });
+  }
+  const conduitDbPath = join115(cleoDir, "conduit.db");
+  if (existsSync118(conduitDbPath)) {
+    findings.push({
+      check: "conduit.db",
+      status: "ok",
+      details: "conduit.db exists"
+    });
+  } else {
+    findings.push({
+      check: "conduit.db",
+      status: "warning",
+      details: "conduit.db not found",
+      fix: "Run: cleo upgrade"
+    });
+  }
+  const memoryBridgePath = join115(cleoDir, "memory-bridge.md");
+  if (existsSync118(memoryBridgePath)) {
+    try {
+      const content = readFileSync86(memoryBridgePath, "utf-8");
+      const hasAutoGenMarker = content.includes("Auto-generated");
+      const hasGarbage = content.includes("undefined") && content.length < 100;
+      if (hasGarbage) {
+        findings.push({
+          check: "memory-bridge.md",
+          status: "error",
+          details: "memory-bridge.md contains garbage content",
+          fix: "Run: cleo upgrade (will regenerate)"
+        });
+      } else if (hasAutoGenMarker) {
+        findings.push({
+          check: "memory-bridge.md",
+          status: "ok",
+          details: "memory-bridge.md exists and has valid content"
+        });
+      } else {
+        findings.push({
+          check: "memory-bridge.md",
+          status: "warning",
+          details: "memory-bridge.md exists but may be stale (no auto-generated marker)",
+          fix: "Run: cleo upgrade (will regenerate)"
+        });
+      }
+    } catch {
+      findings.push({
+        check: "memory-bridge.md",
+        status: "warning",
+        details: "memory-bridge.md exists but could not be read"
+      });
+    }
+  } else {
+    findings.push({
+      check: "memory-bridge.md",
+      status: "warning",
+      details: "memory-bridge.md not found",
+      fix: "Run: cleo upgrade (will regenerate)"
     });
   }
   const okCount = findings.filter((f2) => f2.status === "ok").length;
@@ -112118,6 +112319,7 @@ __export(internal_exports, {
   attachAgentToProject: () => attachAgentToProject2,
   auditData: () => auditData,
   auditLog: () => auditLog,
+  autoLinkMemories: () => autoLinkMemories,
   autoRecordDispatchTokenUsage: () => autoRecordDispatchTokenUsage,
   backfillBrainGraph: () => backfillBrainGraph,
   backfillTasks: () => backfillTasks,
@@ -112531,12 +112733,14 @@ __export(internal_exports, {
   lifecycleStageNameSchema: () => lifecycleStageNameSchema,
   lifecycleStageStatusSchema: () => lifecycleStageStatusSchema,
   lifecycleTransitionTypeSchema: () => lifecycleTransitionTypeSchema,
+  linkMemoryToCode: () => linkMemoryToCode,
   listAdrs: () => listAdrs,
   listAgentInstances: () => listAgentInstances,
   listAgentsForProject: () => listAgentsForProject,
   listBackups: () => listBackups,
   listBrainBackups: () => listBrainBackups,
   listChains: () => listChains,
+  listCodeLinks: () => listCodeLinks,
   listEpicsWithLifecycle: () => listEpicsWithLifecycle,
   listGlobalSaltBackups: () => listGlobalSaltBackups,
   listGlobalSqliteBackups: () => listGlobalSqliteBackups,
@@ -112660,6 +112864,8 @@ __export(internal_exports, {
   pushRelease: () => pushRelease,
   pushWarning: () => pushWarning,
   queryAudit: () => queryAudit,
+  queryCodeForMemory: () => queryCodeForMemory,
+  queryMemoriesForCode: () => queryMemoriesForCode,
   readGrades: () => readGrades,
   readJson: () => readJson,
   readManifestEntries: () => readManifestEntries2,
@@ -113017,6 +113223,7 @@ var init_internal = __esm({
     init_init();
     init_auto_extract();
     init_brain_embedding();
+    init_graph_memory_bridge();
     init_llm_extraction();
     init_memory_bridge();
     init_session_memory();
@@ -124647,26 +124854,58 @@ var init_memory2 = __esm({
             }
             case "code.links": {
               const { listCodeLinks: listCodeLinks2 } = await Promise.resolve().then(() => (init_internal(), internal_exports));
-              const result = await listCodeLinks2(projectRoot);
-              return wrapResult(result, "query", "memory", operation, startTime);
+              const links = await listCodeLinks2(projectRoot);
+              return wrapResult(
+                { success: true, data: links },
+                "query",
+                "memory",
+                operation,
+                startTime
+              );
             }
             case "code.memories-for-code": {
               const symbol2 = params?.symbol;
               if (!symbol2) {
-                return errorResult("query", "memory", operation, "E_INVALID_INPUT", "symbol is required", startTime);
+                return errorResult(
+                  "query",
+                  "memory",
+                  operation,
+                  "E_INVALID_INPUT",
+                  "symbol is required",
+                  startTime
+                );
               }
               const { queryMemoriesForCode: queryMemoriesForCode2 } = await Promise.resolve().then(() => (init_internal(), internal_exports));
               const result = await queryMemoriesForCode2(projectRoot, symbol2);
-              return wrapResult({ success: true, data: result }, "query", "memory", operation, startTime);
+              return wrapResult(
+                { success: true, data: result },
+                "query",
+                "memory",
+                operation,
+                startTime
+              );
             }
             case "code.for-memory": {
               const memoryId = params?.memoryId;
               if (!memoryId) {
-                return errorResult("query", "memory", operation, "E_INVALID_INPUT", "memoryId is required", startTime);
+                return errorResult(
+                  "query",
+                  "memory",
+                  operation,
+                  "E_INVALID_INPUT",
+                  "memoryId is required",
+                  startTime
+                );
               }
               const { queryCodeForMemory: queryCodeForMemory2 } = await Promise.resolve().then(() => (init_internal(), internal_exports));
               const result = await queryCodeForMemory2(projectRoot, memoryId);
-              return wrapResult({ success: true, data: result }, "query", "memory", operation, startTime);
+              return wrapResult(
+                { success: true, data: result },
+                "query",
+                "memory",
+                operation,
+                startTime
+              );
             }
             default:
               return unsupportedOp("query", "memory", operation, startTime);
@@ -124842,16 +125081,35 @@ var init_memory2 = __esm({
               const memoryId = params?.memoryId;
               const codeSymbol = params?.codeSymbol;
               if (!memoryId || !codeSymbol) {
-                return errorResult("mutate", "memory", operation, "E_INVALID_INPUT", "memoryId and codeSymbol are required", startTime);
+                return errorResult(
+                  "mutate",
+                  "memory",
+                  operation,
+                  "E_INVALID_INPUT",
+                  "memoryId and codeSymbol are required",
+                  startTime
+                );
               }
               const { linkMemoryToCode: linkMemoryToCode2 } = await Promise.resolve().then(() => (init_internal(), internal_exports));
               const linked = await linkMemoryToCode2(projectRoot, memoryId, codeSymbol);
-              return wrapResult({ success: true, data: { linked } }, "mutate", "memory", operation, startTime);
+              return wrapResult(
+                { success: true, data: { linked } },
+                "mutate",
+                "memory",
+                operation,
+                startTime
+              );
             }
             case "code.auto-link": {
               const { autoLinkMemories: autoLinkMemories2 } = await Promise.resolve().then(() => (init_internal(), internal_exports));
               const result = await autoLinkMemories2(projectRoot);
-              return wrapResult({ success: true, data: result }, "mutate", "memory", operation, startTime);
+              return wrapResult(
+                { success: true, data: result },
+                "mutate",
+                "memory",
+                operation,
+                startTime
+              );
             }
             default:
               return unsupportedOp("mutate", "memory", operation, startTime);
@@ -140901,6 +141159,37 @@ async function runPostUpdateDiagnostics(opts) {
       );
     }
   } else {
+    if (!opts?.skipUpgrade) {
+      const result = await runUpgrade({ autoMigrate: false });
+      if (result.applied > 0 || result.errors.length > 0) {
+        if (result.actions.length > 0) {
+          process.stderr.write("Post-update maintenance:\n");
+          for (const action of result.actions) {
+            if (action.status === "skipped") continue;
+            const icon = action.status === "applied" ? "  \u2713" : action.status === "error" ? "  \u2717" : "  -";
+            process.stderr.write(`${icon} ${action.action}: ${action.details}
+`);
+          }
+          process.stderr.write("\n");
+        }
+        cliOutput(
+          {
+            postUpdate: true,
+            upgrade: {
+              success: result.success,
+              applied: result.applied,
+              actions: result.actions,
+              errors: result.errors.length > 0 ? result.errors : void 0
+            }
+          },
+          {
+            command: "self-update",
+            message: result.success ? `Post-update maintenance complete (${result.applied} action(s) applied).` : "Post-update maintenance had errors."
+          }
+        );
+        return;
+      }
+    }
     cliOutput(
       {
         postUpdate: true,