feat(coding-agent): package deduplication and collision detection

- Package deduplication: same package in global+project, project wins
- Collision detection for skills, prompts, and themes with ResourceCollision type
- PathMetadata tracking with parent directory lookup for file paths
- Display improvements: section headers, sorted groups, accent colors for packages
- pi list shows full paths below package names
- Extension loader discovers files in directories without index.ts
- In-memory SettingsManager properly tracks project settings

fixes #645

packages/coding-agent/CHANGELOG.md

@@ -19,6 +19,8 @@
 - Glob pattern support with minimatch in package filters, top-level settings arrays, and pi manifest (e.g., `"!funky.json"`, `"*.ts"`) ([#645](https://github.com/badlogic/pi-mono/issues/645))
 - `/reload` command to reload extensions, skills, prompts, and themes ([#645](https://github.com/badlogic/pi-mono/issues/645))
 - CLI flags for `--skill`, `--prompt-template`, `--theme`, `--no-prompt-templates`, and `--no-themes` ([#645](https://github.com/badlogic/pi-mono/issues/645))
+- Package deduplication: if same package appears in global and project settings, project wins ([#645](https://github.com/badlogic/pi-mono/issues/645))
+- Unified collision reporting with `ResourceDiagnostic` type for all resource types ([#645](https://github.com/badlogic/pi-mono/issues/645))
 - Show provider alongside the model in the footer if multiple providers are available
 
 ### Changed