fix(sync): Adopt only directories that contain a SKILL.md

packages/dotagents/src/cli/commands/sync.test.ts

@@ -79,6 +79,43 @@ describe("runSync", () => {
     expect(config.skills).toHaveLength(2);
   });
 
+  it("adopts only directories that are valid skills", async () => {
+    await writeFile(join(projectRoot, "agents.toml"), "version = 1\n");
+    const skillsDir = join(projectRoot, ".agents", "skills");
+    // Directories another tool keeps under a migrated .claude/skills/
+    await mkdir(join(skillsDir, ".trash", "old"), { recursive: true });
+    await writeFile(join(skillsDir, ".trash", "old", "SKILL.md"), SKILL_MD("old"));
+    await mkdir(join(skillsDir, "synced", "bucket", "pdf"), { recursive: true });
+    await writeFile(join(skillsDir, "synced", "bucket", "pdf", "SKILL.md"), SKILL_MD("pdf"));
+    await mkdir(join(skillsDir, "notes"), { recursive: true });
+    await writeFile(join(skillsDir, "notes", "README.md"), "notes\n");
+    await mkdir(join(skillsDir, "review"), { recursive: true });
+    await writeFile(join(skillsDir, "review", "SKILL.md"), SKILL_MD("review"));
+
+    const result = await runSync({ scope: resolveScope("project", projectRoot) });
+
+    expect(result.adopted).toEqual(["review"]);
+    const config = await loadConfig(join(projectRoot, "agents.toml"));
+    expect(config.skills.map((s) => s.name)).toEqual(["review"]);
+  });
+
+  it("forgets an adopted skill whose directory no longer has a SKILL.md", async () => {
+    await writeFile(join(projectRoot, "agents.toml"), "version = 1\n");
+    await mkdir(join(projectRoot, ".agents", "skills", "notes"), { recursive: true });
+    await writeFile(join(projectRoot, ".agents", "skills", "notes", "README.md"), "notes\n");
+    await writeLockfile(join(projectRoot, "agents.lock"), {
+      version: 1,
+      skills: { notes: { source: "path:.agents/skills/notes" } },
+    });
+
+    const result = await runSync({ scope: resolveScope("project", projectRoot) });
+
+    expect(result.adopted).toEqual([]);
+    expect((await loadLockfile(join(projectRoot, "agents.lock")))!.skills).toEqual({});
+    const gitignore = await readFile(join(projectRoot, ".agents", ".gitignore"), "utf-8");
+    expect(gitignore).not.toContain("/skills/notes");
+  });
+
   it("ignores plugin skill ownership markers when adopting orphaned skills", async () => {
     await writeFile(join(projectRoot, "agents.toml"), "version = 1\n");
     const markerDir = join(projectRoot, ".agents", "skills", ".dotagents-managed");

packages/dotagents/src/cli/commands/sync.ts

@@ -95,10 +95,10 @@ export async function runSync(opts: SyncOptions): Promise<SyncResult> {
   // 1. Adopt orphaned skills (installed but not in agents.toml)
   if (existsSync(skillsDir)) {
     const adoptedLockEntries: Record<string, { source: string }> = {};
+    let forgotten = false;
     const entries = await readdir(skillsDir, { withFileTypes: true });
     for (const entry of entries) {
       if (!entry.isDirectory()) {continue;}
-      if (entry.name === ".dotagents-managed") {continue;}
       if (declaredNames.has(entry.name)) {continue;}
 
       const locked = lockfile?.skills[entry.name];
@@ -111,6 +111,19 @@ export async function runSync(opts: SyncOptions): Promise<SyncResult> {
         continue;
       }
 
+      // Only adopt skill directories. Ownership markers, hidden directories, and
+      // folders without a SKILL.md (e.g. Claude Code's synced/ and .trash/ after
+      // .claude/skills/ is migrated) are not skills.
+      const skillPath = managedSkillPath(skillsDir, entry.name);
+      if (!skillPath || !existsSync(join(skillPath, "SKILL.md"))) {
+        // Drop a leftover in-place lock entry so .agents/.gitignore does not hide the folder.
+        if (locked) {
+          delete lockfile!.skills[entry.name];
+          forgotten = true;
+        }
+        continue;
+      }
+
       const sourcePrefix = scope.scope === "user" ? "path:skills/" : "path:.agents/skills/";
       const source = `${sourcePrefix}${entry.name}`;
       await addSkillToConfig(configPath, entry.name, { source });
@@ -120,7 +133,7 @@ export async function runSync(opts: SyncOptions): Promise<SyncResult> {
       adopted.push(entry.name);
     }
 
-    if (adopted.length > 0 || pruned.length > 0) {
+    if (adopted.length > 0 || pruned.length > 0 || forgotten) {
       lockfile = {
         version: 1,
         skills: { ...lockfile?.skills, ...adoptedLockEntries },

specs/SPEC.md

@@ -647,7 +647,7 @@ dotagents sync
 ```
 
 **Behavior:**
-1. Adopt orphaned local skills (installed but not in `agents.toml`, and not previously managed) into config
+1. Adopt orphaned local skills (directories with a valid skill name and a `SKILL.md`, installed but not in `agents.toml`, and not previously managed) into config
 2. Prune stale managed skills that were removed from config but still exist on disk locally
 3. In project scope, regenerate `.agents/.gitignore`
 4. In project scope, warn if `agents.lock` and `.agents/.gitignore` are not in the root `.gitignore`