feat(FN-3882): document clearStaleBlockedBy() in SelfHealingManager section

Added a single line documenting `clearStaleBlockedBy()` in the SelfHealingManager section of the architecture docs.

Fusion-Task-Id: FN-3882

.changeset/FN-3862-merge-attribution.md

@@ -0,0 +1,5 @@
+---
+"@runfusion/fusion": patch
+---
+
+Stop overwriting canonical merge commit SHAs on already-done tasks during self-healing reconciliation. Confirmed `mergeDetails.commitSha` is now preserved as authoritative; rediscovery for unconfirmed done tasks prefers the earliest owned commit so the original merge commit wins over later follow-up commits sharing the same `Fusion-Task-Id` trailer.

.changeset/FN-3868-github-tracking-settings.md

@@ -0,0 +1,5 @@
+---
+"@runfusion/fusion": patch
+---
+
+Add global and project settings for GitHub issue tracking: global default tracking repo, project-level default tracking repo, per-project tracking toggle for new tasks, GitHub auth mode (`gh-cli` | `token`), and optional stored personal access token. This is foundational settings work for FN-3868 → FN-3876; behavior wiring ships in downstream subtasks.

.changeset/FN-3877-triage-spec-compaction.md

@@ -0,0 +1,5 @@
+---
+"@runfusion/fusion": patch
+---
+
+Triage: progressively compact large optional sections (subtask guidance, attachments, existing spec, user comments) of the spec prompt when the model's context window overflows, in addition to the existing project-memory compaction. Fixes failures on small-context models such as local vLLM Qwen3-30B (issue Runfusion/Fusion#62, FN-3877).

.changeset/FN-3879-checkout-columns-self-heal.md

@@ -0,0 +1,7 @@
+---
+"@runfusion/fusion": patch
+---
+
+Add a compatibility self-heal for legacy task databases that report `schemaVersion >= 20` but are missing checkout lease columns (`checkedOutBy`, `checkedOutAt`, `checkoutNodeId`, `checkoutRunId`, `checkoutLeaseRenewedAt`, `checkoutLeaseEpoch`).
+
+On initialization, missing lease columns are now added idempotently before version-guarded migrations, matching the earlier `nodeId` mitigation pattern and preventing `no such column: checkoutNodeId` crashes in task listing paths.

.changeset/fn-3783-reports-review-panel.md

@@ -0,0 +1,5 @@
+---
+"@runfusion/fusion": patch
+---
+
+Add a multi-agent report review panel flow to the bundled reports plugin, including parallel reviewer orchestration, structured feedback parsing with retry, deterministic aggregation, and documented timeout/failure semantics.

.changeset/fn-3864-paused-scope-exclusion.md

@@ -0,0 +1,5 @@
+---
+"@runfusion/fusion": patch
+---
+
+Scheduler: exclude paused in-review tasks from `activeScopes`. Paused failed-merge tasks no longer block dispatch of overlapping todo tasks via `blockedBy` re-stamping. (FN-3867)

.changeset/fn-3864-recover-already-merged-review.md

@@ -0,0 +1,5 @@
+---
+"@runfusion/fusion": patch
+---
+
+Add `recoverAlreadyMergedReviewTasks()` self-healing sweep to recover phantom-merge-guard false positives. Detects tasks whose content already landed on the integration branch (via Fusion-Task-Id trailer, branch ancestry, or git patch-id walk) and reconciles them to `done` with proper merge metadata.

.changeset/fn-3878-restore-commitsha.md

@@ -0,0 +1,5 @@
+---
+"@runfusion/fusion": patch
+---
+
+Restore canonical mergeDetails.commitSha for tasks FN-3794, FN-3814, FN-3829 whose attribution had been overwritten by self-healing reconciliation prior to the FN-3862 fix. Adds an idempotent restoration script (`scripts/restore-merge-sha-fn-3878.mjs`) for operators to re-verify or repair similar drift.

.changeset/fn-3879-chat-rooms-wired.md

@@ -0,0 +1,5 @@
+---
+"@runfusion/fusion": patch
+---
+
+Wire chat rooms UI to backend. Creating a room now persists via /api/chat/rooms, the sidebar lists real rooms, room threads load history and stream new messages over chat:room:* SSE events, and the FN-3807 "Coming soon" placeholder is gone.

packages/cli/src/__tests__/bundle-output.test.ts

@@ -158,15 +158,24 @@ describe("CLI bundle output", () => {
     expect(existsSync(join(stagedRoot, "src", "process-manager.ts"))).toBe(true);
   });
 
-  it("dist/plugins/fusion-plugin-dependency-graph/ is staged with a valid manifest", () => {
+  it("dist/plugins/fusion-plugin-dependency-graph/ is staged as bundled runtime output", () => {
     const stagedRoot = join(cliRoot, "dist", "plugins", "fusion-plugin-dependency-graph");
     const manifestPath = join(stagedRoot, "manifest.json");
+    const packageJsonPath = join(stagedRoot, "package.json");
 
     expect(existsSync(manifestPath)).toBe(true);
     const manifest = JSON.parse(readFileSync(manifestPath, "utf-8")) as { id?: string; name?: string };
     expect(manifest.id).toBe("fusion-plugin-dependency-graph");
     expect(typeof manifest.name).toBe("string");
     expect(manifest.name?.length).toBeGreaterThan(0);
+
+    expect(existsSync(join(stagedRoot, "bundled.js"))).toBe(true);
+    expect(existsSync(join(stagedRoot, "src"))).toBe(false);
+
+    const stagedPkg = JSON.parse(readFileSync(packageJsonPath, "utf-8")) as {
+      exports?: { "."?: { import?: string } };
+    };
+    expect(stagedPkg.exports?.["."]?.import).toBe("./bundled.js");
   });
 
   it("dist/plugins/fusion-plugin-whatsapp-chat/ is staged with a valid manifest", () => {

packages/cli/src/__tests__/package-config.test.ts

@@ -98,17 +98,20 @@ describe("CLI package.json publishing config", () => {
     );
 
     function extractStringArray(name: string): string[] {
-      const m = tsupRaw.match(new RegExp(`${name}:\\s*\\[([\\s\\S]*?)\\]`, "m"));
-      if (!m) return [];
-      return [...m[1].matchAll(/["']([^"']+)["']/g)].map((mm) => mm[1]);
+      const matches = [...tsupRaw.matchAll(new RegExp(`${name}:\\s*\\[([\\s\\S]*?)\\]`, "gm"))];
+      const values = matches.flatMap((m) =>
+        [...m[1].matchAll(/["']([^"']+)["']/g)].map((mm) => mm[1]),
+      );
+      return [...new Set(values)];
     }
 
     function extractRegexes(name: string): RegExp[] {
-      const m = tsupRaw.match(new RegExp(`${name}:\\s*\\[([\\s\\S]*?)\\]`, "m"));
-      if (!m) return [];
+      const matches = [...tsupRaw.matchAll(new RegExp(`${name}:\\s*\\[([\\s\\S]*?)\\]`, "gm"))];
       // Match `/PATTERN/flags` where PATTERN may contain escaped slashes (`\/`).
-      return [...m[1].matchAll(/\/((?:\\\/|[^/\n])+)\/[gimsuy]*/g)].map(
-        (mm) => new RegExp(mm[1].replace(/\\\//g, "/")),
+      return matches.flatMap((m) =>
+        [...m[1].matchAll(/\/((?:\\\/|[^/\n])+)\/[gimsuy]*/g)].map(
+          (mm) => new RegExp(mm[1].replace(/\\\//g, "/")),
+        ),
       );
     }
 
@@ -125,6 +128,8 @@ describe("CLI package.json publishing config", () => {
       "cpu-features": "transitive dep of dockerode (via ssh2)",
       "@homebridge/node-pty-prebuilt-multiarch":
         "aliased as node-pty in dependencies; the alias entry satisfies the import",
+      "@fusion/core": "plugin-entry bundling external only; not a runtime dep of the CLI bin",
+      "@fusion/engine": "plugin-entry bundling external only; not a runtime dep of the CLI bin",
     };
 
     it("parses externals from tsup.config.ts", () => {

packages/cli/src/plugins/__tests__/bundled-plugin-install.test.ts

@@ -195,9 +195,9 @@ beforeEach(() => {
 });
 
 describe("resolvePluginEntryPath", () => {
-  it("prefers src/index.ts over bundled.js when both exist in workspace contexts", () => {
+  it("prefers bundled.js when both bundled and source entries exist", () => {
     mockExistsSync.mockImplementation((p: string) => p.endsWith("/src/index.ts") || p.endsWith("/bundled.js"));
-    expect(resolvePluginEntryPath("/tmp/plugin")).toBe("/tmp/plugin/src/index.ts");
+    expect(resolvePluginEntryPath("/tmp/plugin")).toBe("/tmp/plugin/bundled.js");
   });
 
   it("prefers bundled.js when source entry is unavailable", () => {
@@ -205,14 +205,14 @@ describe("resolvePluginEntryPath", () => {
     expect(resolvePluginEntryPath("/tmp/plugin")).toBe("/tmp/plugin/bundled.js");
   });
 
-  it("prefers src/index.ts over dist/index.js in workspace contexts", () => {
+  it("prefers dist/index.js when bundled.js is unavailable", () => {
     mockExistsSync.mockImplementation((p: string) => p.endsWith("/src/index.ts") || p.endsWith("/dist/index.js"));
-    expect(resolvePluginEntryPath("/tmp/plugin")).toBe("/tmp/plugin/src/index.ts");
+    expect(resolvePluginEntryPath("/tmp/plugin")).toBe("/tmp/plugin/dist/index.js");
   });
 
-  it("falls back to dist/index.js when source entry is unavailable", () => {
-    mockExistsSync.mockImplementation((p: string) => p.endsWith("/dist/index.js"));
-    expect(resolvePluginEntryPath("/tmp/plugin")).toBe("/tmp/plugin/dist/index.js");
+  it("falls back to src/index.ts for workspace-dev plugins without build outputs", () => {
+    mockExistsSync.mockImplementation((p: string) => p.endsWith("/src/index.ts"));
+    expect(resolvePluginEntryPath("/tmp/plugin")).toBe("/tmp/plugin/src/index.ts");
   });
 });
 
@@ -412,10 +412,11 @@ describe("ensureBundledDependencyGraphPluginInstalled", () => {
     );
   });
 
-  it("registers Hermes from source entry when both src and dist entries exist", async () => {
+  it("registers Hermes from bundled.js when bundled, src, and dist entries all exist", async () => {
     const manifest = makeManifest({ id: HERMES_PLUGIN_ID, name: "Hermes Runtime" });
     mockExistsSync.mockImplementation((p: string) => {
       if (p.endsWith("manifest.json") && p.includes(HERMES_PLUGIN_ID)) return true;
+      if (p.endsWith("/bundled.js") && p.includes(HERMES_PLUGIN_ID)) return true;
       if (p.endsWith("/src/index.ts") && p.includes(HERMES_PLUGIN_ID)) return true;
       if (p.endsWith("/dist/index.js") && p.includes(HERMES_PLUGIN_ID)) return true;
       return false;
@@ -434,6 +435,6 @@ describe("ensureBundledDependencyGraphPluginInstalled", () => {
 
     expect(result).toBe("installed");
     const registerCall = store.registerPlugin.mock.calls[0]?.[0] as { path: string };
-    expect(registerCall.path).toContain(`${HERMES_PLUGIN_ID}/src/index.ts`);
+    expect(registerCall.path).toContain(`${HERMES_PLUGIN_ID}/bundled.js`);
   });
 });

packages/cli/src/plugins/bundled-plugin-install.ts

@@ -64,16 +64,16 @@ function resolveBundledPluginDir(pluginId: string): string | null {
  * Resolve the actual loadable entry FILE path for a plugin directory. Node ESM
  * does not allow directory imports, so we must register the explicit file the
  * loader will dynamic-import. Preference order:
- *   1. ./src/index.ts (workspace/dev source of truth)
- *   2. ./bundled.js   (esbuild-bundled, ships in npm tarball)
- *   3. ./dist/index.js
+ *   1. ./bundled.js   (esbuild-bundled, shipped in npm tarball)
+ *   2. ./dist/index.js (legacy prebuilt fallback)
+ *   3. ./src/index.ts (workspace/dev fallback when no bundle exists)
  *   4. fall back to the directory itself
  */
 export function resolvePluginEntryPath(pluginDir: string): string {
   const candidates = [
-    join(pluginDir, "src", "index.ts"),
     join(pluginDir, "bundled.js"),
     join(pluginDir, "dist", "index.js"),
+    join(pluginDir, "src", "index.ts"),
   ];
   for (const candidate of candidates) {
     if (existsSync(candidate)) {

packages/cli/tsup.config.ts

@@ -54,6 +54,76 @@ const dashboardClientStub = `<!doctype html>
 </html>
 `;
 
+type BundlePluginEntryOptions = {
+  pluginId: string;
+  srcDir: string;
+  destDir: string;
+  withMcpAsset?: boolean;
+};
+
+async function bundlePluginEntry({ pluginId, srcDir, destDir, withMcpAsset = false }: BundlePluginEntryOptions) {
+  if (existsSync(destDir)) {
+    rmSync(destDir, { recursive: true, force: true });
+  }
+  if (!existsSync(srcDir)) {
+    console.warn(
+      `WARNING: Plugin source not found at ${srcDir}; ${pluginId} will be unavailable in the published package.`,
+    );
+    return;
+  }
+
+  mkdirSync(destDir, { recursive: true });
+  cpSync(join(srcDir, "manifest.json"), join(destDir, "manifest.json"));
+
+  const srcPkg = JSON.parse(readFileSync(join(srcDir, "package.json"), "utf-8"));
+  const destPkg = {
+    name: srcPkg.name,
+    version: srcPkg.version,
+    type: "module",
+    exports: { ".": { import: "./bundled.js" } },
+    private: true,
+  };
+  writeFileSync(join(destDir, "package.json"), JSON.stringify(destPkg, null, 2));
+
+  const srcEntry = join(srcDir, "src", "index.ts");
+  const builtEntry = join(srcDir, "dist", "index.js");
+  const entry = existsSync(srcEntry) ? srcEntry : builtEntry;
+  if (!existsSync(entry)) {
+    throw new Error(`No entry found for ${pluginId} (looked for src/index.ts and dist/index.js)`);
+  }
+
+  await esbuildBuild({
+    entryPoints: [entry],
+    bundle: true,
+    format: "esm",
+    platform: "node",
+    target: "node22",
+    outfile: join(destDir, "bundled.js"),
+    external: ["@fusion/core", "@fusion/engine"],
+    alias: {
+      "@fusion/plugin-sdk": join(__dirname, "..", "plugin-sdk", "src", "index.ts"),
+    },
+    logLevel: "warning",
+  });
+
+  if (withMcpAsset) {
+    const mcpServerAsset = join(srcDir, "src", "mcp-schema-server.cjs");
+    if (!existsSync(mcpServerAsset)) {
+      throw new Error(
+        `[tsup] Missing required bridge asset for ${pluginId} at ${mcpServerAsset}; expected committed source file mcp-schema-server.cjs.`,
+      );
+    }
+    cpSync(mcpServerAsset, join(destDir, "mcp-schema-server.cjs"));
+  }
+
+  const bundledOutput = join(destDir, "bundled.js");
+  if (!existsSync(bundledOutput)) {
+    throw new Error(`[tsup] Missing bundled output for ${pluginId}: expected ${bundledOutput}`);
+  }
+
+  console.log(`Bundled plugin ${pluginId} to dist/plugins/${pluginId}/bundled.js`);
+}
+
 export default defineConfig({
   entry: ["src/bin.ts", "src/extension.ts"],
   format: ["esm"],
@@ -137,20 +207,11 @@ export default defineConfig({
       );
     }
 
-    if (existsSync(dependencyGraphPluginDest)) {
-      rmSync(dependencyGraphPluginDest, { recursive: true, force: true });
-    }
-    if (existsSync(dependencyGraphPluginSrc)) {
-      mkdirSync(dependencyGraphPluginDest, { recursive: true });
-      cpSync(join(dependencyGraphPluginSrc, "manifest.json"), join(dependencyGraphPluginDest, "manifest.json"));
-      cpSync(join(dependencyGraphPluginSrc, "package.json"), join(dependencyGraphPluginDest, "package.json"));
-      cpSync(join(dependencyGraphPluginSrc, "src"), join(dependencyGraphPluginDest, "src"), { recursive: true });
-      console.log("Copied dependency graph plugin to dist/plugins/fusion-plugin-dependency-graph/");
-    } else {
-      console.warn(
-        `WARNING: Dependency graph plugin source not found at ${dependencyGraphPluginSrc}; bundled auto-install will be unavailable.`,
-      );
-    }
+    await bundlePluginEntry({
+      pluginId: "fusion-plugin-dependency-graph",
+      srcDir: dependencyGraphPluginSrc,
+      destDir: dependencyGraphPluginDest,
+    });
 
     if (existsSync(whatsappChatPluginDest)) {
       rmSync(whatsappChatPluginDest, { recursive: true, force: true });
@@ -200,71 +261,12 @@ export default defineConfig({
     // Bundle each runtime plugin into a self-contained ESM file so npm/npx
     // installs can load them without the workspace `@fusion/plugin-sdk`.
     for (const pluginId of RUNTIME_PLUGIN_IDS) {
-      const pluginSrcDir = join(__dirname, "..", "..", "plugins", pluginId);
-      const pluginDestDir = join(__dirname, "dist", "plugins", pluginId);
-
-      if (existsSync(pluginDestDir)) {
-        rmSync(pluginDestDir, { recursive: true, force: true });
-      }
-      if (!existsSync(pluginSrcDir)) {
-        console.warn(
-          `WARNING: Runtime plugin source not found at ${pluginSrcDir}; ${pluginId} will be unavailable in the published package.`,
-        );
-        continue;
-      }
-
-      mkdirSync(pluginDestDir, { recursive: true });
-
-      cpSync(join(pluginSrcDir, "manifest.json"), join(pluginDestDir, "manifest.json"));
-
-      // Stripped package.json: no dependencies (workspace SDK is inlined into
-      // bundled.js), exports point at the bundle. Keeps the published tarball
-      // self-contained without leaking workspace-only metadata.
-      const srcPkg = JSON.parse(readFileSync(join(pluginSrcDir, "package.json"), "utf-8"));
-      const destPkg = {
-        name: srcPkg.name,
-        version: srcPkg.version,
-        type: "module",
-        exports: { ".": { import: "./bundled.js" } },
-        private: true,
-      };
-      writeFileSync(join(pluginDestDir, "package.json"), JSON.stringify(destPkg, null, 2));
-
-      // Pick the best available entry: built dist/index.js if present, else
-      // raw src/index.ts (esbuild can transpile TS).
-      const builtEntry = join(pluginSrcDir, "dist", "index.js");
-      const srcEntry = join(pluginSrcDir, "src", "index.ts");
-      const entry = existsSync(builtEntry) ? builtEntry : srcEntry;
-
-      if (!existsSync(entry)) {
-        console.warn(`WARNING: No entry found for ${pluginId} (looked for dist/index.js and src/index.ts)`);
-        continue;
-      }
-
-      await esbuildBuild({
-        entryPoints: [entry],
-        bundle: true,
-        format: "esm",
-        platform: "node",
-        target: "node22",
-        outfile: join(pluginDestDir, "bundled.js"),
-        // @fusion/core and @fusion/engine are loaded by the host process at
-        // runtime; the SDK is inlined.
-        external: ["@fusion/core", "@fusion/engine"],
-        logLevel: "warning",
+      await bundlePluginEntry({
+        pluginId,
+        srcDir: join(__dirname, "..", "..", "plugins", pluginId),
+        destDir: join(__dirname, "dist", "plugins", pluginId),
+        withMcpAsset: RUNTIME_PLUGINS_WITH_MCP_SCHEMA_SERVER.has(pluginId),
       });
-
-      if (RUNTIME_PLUGINS_WITH_MCP_SCHEMA_SERVER.has(pluginId)) {
-        const mcpServerAsset = join(pluginSrcDir, "src", "mcp-schema-server.cjs");
-        if (!existsSync(mcpServerAsset)) {
-          throw new Error(
-            `[tsup] Missing required bridge asset for ${pluginId} at ${mcpServerAsset}; expected committed source file mcp-schema-server.cjs.`,
-          );
-        }
-        cpSync(mcpServerAsset, join(pluginDestDir, "mcp-schema-server.cjs"));
-      }
-
-      console.log(`Bundled runtime plugin ${pluginId} to dist/plugins/${pluginId}/bundled.js`);
     }
 
     if (existsSync(dashboardClientDest)) {