S56: spawn template overhaul + system-wide README push + .gitkeep cleanup (#129)

- Spawn template system rebuilt: regenerate-registry command (3-pass ID matching),
  registry 26→41 files, generate_branch_meta fixed, Phase 0 snapshot added
- System-wide push: 12/12 branches updated (227 additions, 0 errors)
- READMEs added to all standard directories across 15 branches
- .claude/settings.local.json tracked system-wide (deny rules)
- 35 .gitkeep files removed (replaced by READMEs)
- Bypass files updated across 13 branches
- Bugs fixed: manager citizen_class crash, backup rglob performance

Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

src/aipass/cli/apps/README.md

@@ -0,0 +1,8 @@
+# Apps
+
+Application layer for `CLI`.
+
+- `cli.py` — Entry point. Auto-discovers and routes commands to modules.
+- `modules/` — Business logic and orchestration. One module per command.
+- `handlers/` — Implementation details. Called by modules, never by CLI directly.
+- `plugins/` — Scheduled tasks and extensions.

src/aipass/cli/apps/handlers/README.md

@@ -0,0 +1,5 @@
+# Handlers
+
+Implementation details for `CLI`.
+
+Handlers do the actual work. They are called by modules, never directly by the CLI. Keep business logic in modules, implementation in handlers.

src/aipass/cli/apps/modules/README.md

@@ -0,0 +1,5 @@
+# Modules
+
+Business logic for `CLI`. One module per command.
+
+Modules orchestrate work by calling handlers. They are the public API of the branch — drone routes commands here.

src/aipass/cli/apps/plugins/README.md

@@ -0,0 +1,5 @@
+# Plugins
+
+Scheduled tasks and extensions for `CLI`.
+
+Plugins are standalone units of work that can be scheduled via the daemon. Each plugin handles one specific recurring task.