Add manifest.json for update discovery

Updates now fetch manifest.json first to discover all updatable components.
This allows 1.0 users to learn about new files (like commands.md) when they
run "update". Safety-protocol.md bumped to 1.1.0 with update notice for 1.0 users.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

commands.md

@@ -1,4 +1,4 @@
-<!-- version: 1.0.0 -->
+<!-- version: 1.1.0 -->
 # Customization Commands
 
 The client can request changes to their therapy setup during a session. All customization files are stored locally in `.therapy/library/`.
@@ -63,15 +63,28 @@ Recognize conversational requests, not just exact command phrases:
 
 ## When client says "update", "check for updates", or "get latest version"
 
-1. Read `.therapy/version.json` for current versions and `source_url`
-2. Use WebFetch to get files from GitHub raw URLs:
-   - `https://raw.githubusercontent.com/ataglianetti/inner-dialogue/main/safety-protocol.md`
-   - `https://raw.githubusercontent.com/ataglianetti/inner-dialogue/main/commands.md`
-   - Extract `<!-- version: X.Y.Z -->` header from fetched content
-3. Compare with installed versions
-4. Show available updates, recommend safety-protocol updates
-5. Fetch and write updated files to `.therapy/` and `.therapy/library/`
-6. Update version.json
+1. Read `.therapy/version.json` for current versions
+
+2. Fetch the manifest from GitHub:
+   ```
+   https://raw.githubusercontent.com/ataglianetti/inner-dialogue/main/manifest.json
+   ```
+
+3. For each component in manifest, fetch the file and extract its version from `<!-- version: X.Y.Z -->` header
+
+4. Compare with installed versions and show available updates:
+   > **Updates available:**
+   > - safety-protocol: 1.0.0 → 1.1.0 ⚠️ (recommended)
+   > - commands: (new) → 1.0.0
+   >
+   > Apply updates?
+
+5. For approved updates:
+   - Fetch files from GitHub using manifest's `base_url` + `file` path
+   - Write to location specified in manifest's `target`
+   - Update `.therapy/version.json`
+
+6. Always recommend safety-protocol updates (crisis resources should never be stale)
 
 ## When client says "import", "import notes", or "I have files to import"