fix(coding-agent): add force exclude pattern and fix config toggle persistence

- Add `-path` force-exclude pattern (exact path match, highest precedence)
- Change `+path` force-include to exact path match (no glob)
- Manifest-excluded resources are now hidden from config (not toggleable)
- Config toggle uses `+` to enable and `-` to disable
- Settings paths resolve relative to settings.json location:
  - Global: relative to ~/.pi/agent
  - Project: relative to .pi
- Add baseDir to PathMetadata for proper relative path computation
- Update tests for new base directory and pattern behavior

fixes #951

packages/coding-agent/docs/settings.md

@@ -131,6 +131,8 @@ Edit directly or use `/settings` for common options.
 
 These settings define where to load extensions, skills, prompts, and themes from.
 
+Paths in `~/.pi/agent/settings.json` resolve relative to `~/.pi/agent`. Paths in `.pi/settings.json` resolve relative to `.pi`. Absolute paths and `~` are supported.
+
 | Setting | Type | Default | Description |
 |---------|------|---------|-------------|
 | `packages` | array | `[]` | npm/git packages to load resources from |
@@ -140,6 +142,8 @@ These settings define where to load extensions, skills, prompts, and themes from
 | `themes` | string[] | `[]` | Local theme file paths or directories |
 | `enableSkillCommands` | boolean | `true` | Register skills as `/skill:name` commands |
 
+Arrays support glob patterns and exclusions. Use `!pattern` to exclude. Use `+path` to force-include an exact path and `-path` to force-exclude an exact path.
+
 #### packages
 
 String form loads all resources from a package: