chore: gitignore .factory and remove tracked files

The .factory/ directory contains generated skill definitions for
Factory Droid compatibility. These should not be tracked in git,
same as .claude/skills/ and .agents/.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

.gitignore

@@ -6,6 +6,7 @@ bin/gstack-global-discover
 .gstack/
 .claude/skills/
 .agents/
+.factory/
 .context/
 extension/.auth.json
 .gstack-worktrees/