fix(logger): record warnings in debug.log

`log.warn` wrote to the console only and was muted in silent mode, so a
detached SessionStart pull, whose output is discarded, lost every warning:
the stub deploy failure and the legacy prune among them. Warnings now reach
debug.log like debug and error lines. `warnStubNotDeployed` drops the
second `log.debug` call, which printed the line twice under --verbose.

src/__tests__/logger.test.ts

@@ -45,6 +45,14 @@ describe('file transport', () => {
     expect(fs.readFileSync(logFile, 'utf-8')).toContain('[ERROR] something broke');
   });
 
+  it('writes warn to file, even when silent', () => {
+    // A detached SessionStart pull runs silent with its output discarded; its
+    // warnings must still leave a record.
+    setSilent(true);
+    log.warn('stub not deployed');
+    expect(fs.readFileSync(logFile, 'utf-8')).toContain('[WARN] stub not deployed');
+  });
+
   it('includes timestamp', () => {
     log.debug('ts');
     expect(fs.readFileSync(logFile, 'utf-8').trim()).toMatch(/^\d{4}-\d{2}-\d{2}T/);

src/__tests__/pull-skip-sync.test.ts

@@ -319,8 +319,8 @@ describe('pull skip-sync when repo HEAD unchanged', () => {
     expect(log.success).toHaveBeenCalledWith(expect.stringContaining('Already synced at abc1234, skipping'));
     expect(log.warn).toHaveBeenCalledWith(expect.stringContaining('The built-in teamai skill was not deployed'));
     expect(log.warn).toHaveBeenCalledWith(expect.stringContaining('EACCES: permission denied'));
-    // A SessionStart pull runs detached and silent; debug.log is its only record.
-    expect(log.debug).toHaveBeenCalledWith(expect.stringContaining('The built-in teamai skill was not deployed: EACCES: permission denied'));
+    // `log.warn` also records to debug.log; a second `log.debug` would print it twice under --verbose.
+    expect(log.debug).not.toHaveBeenCalledWith(expect.stringContaining('The built-in teamai skill was not deployed'));
   });
 
   it('warns when the built-in stub cannot be deployed on a full sync', async () => {
@@ -333,8 +333,8 @@ describe('pull skip-sync when repo HEAD unchanged', () => {
 
     expect(log.warn).toHaveBeenCalledWith(expect.stringContaining('The built-in teamai skill was not deployed'));
     expect(log.warn).toHaveBeenCalledWith(expect.stringContaining('EACCES: permission denied'));
-    // A SessionStart pull runs detached and silent; debug.log is its only record.
-    expect(log.debug).toHaveBeenCalledWith(expect.stringContaining('The built-in teamai skill was not deployed: EACCES: permission denied'));
+    // `log.warn` also records to debug.log; a second `log.debug` would print it twice under --verbose.
+    expect(log.debug).not.toHaveBeenCalledWith(expect.stringContaining('The built-in teamai skill was not deployed'));
   });
 
   it('should do full sync when HEAD rev differs from lastPullRev', async () => {

src/pull.ts

@@ -732,13 +732,11 @@ async function reconcileEnvForUnchangedRepo(
 
 /**
  * The stub is the agent's only way into TeamAI, so a failure to deploy it is
- * not silent. A SessionStart pull runs detached with its output discarded, and
- * `log.warn` is muted there, so debug.log keeps the record.
+ * not silent. A SessionStart pull runs detached with its output discarded;
+ * `log.warn` also records to debug.log, which keeps the trace there.
  */
 function warnStubNotDeployed(scopeLabel: string, e: unknown): void {
-  const message = `[${scopeLabel}] The built-in teamai skill was not deployed: ${e instanceof Error ? e.message : String(e)}`;
-  log.warn(message);
-  log.debug(message);
+  log.warn(`[${scopeLabel}] The built-in teamai skill was not deployed: ${e instanceof Error ? e.message : String(e)}`);
 }
 
 async function pullForScope(

src/utils/logger.ts

@@ -10,7 +10,7 @@ let stderrMode = false;
 
 // ─── File transport ─────────────────────────────────────
 //
-//  All log.debug() and log.error() calls are persisted to
+//  All log.debug(), log.warn() and log.error() calls are persisted to
 //  ~/.teamai/debug.log via synchronous append.  This ensures
 //  hook processes (short-lived, stdout swallowed by Claude Code)
 //  leave a durable trace for troubleshooting.
@@ -143,6 +143,7 @@ export const log = {
     writeInfoLine(`${chalk.green('✔')} ${msg}`);
   },
   warn(msg: string): void {
+    writeToFile('WARN', msg);
     if (silentMode) return;
     writeInfoLine(`${chalk.yellow('⚠')} ${msg}`);
   },