docs(plugin): explain updates and Git recovery

docs/src/content/docs/docs/getting-started/quick-start.mdx

@@ -36,6 +36,13 @@ On an interactive terminal, choose project or user scope, select the clients
 that should receive the plugin, review the declaration, and confirm. For
 scripts, provide the target explicitly:
 
+```bash
+allagents plugin install code-review@claude-plugins-official \
+  --scope project --client claude --yes
+```
+
+To install the same plugin for both Claude Code and Codex, run:
+
 ```bash
 allagents plugin install code-review@claude-plugins-official \
   --scope project --client claude,codex --yes
@@ -47,6 +54,20 @@ allagents plugin install code-review@claude-plugins-official \
 allagents update
 ```
 
+Installed file copies follow their declared source. Updates can overwrite edits
+made directly to those copies without asking. Keep lasting customizations in a
+source directory or fork; see [Updates and Local Customizations](/docs/guides/plugins/#updates-and-local-customizations)
+for Git snapshots and recovery.
+
+## Remove a Plugin
+
+```bash
+allagents plugin uninstall code-review@claude-plugins-official --scope project
+```
+
+This removes the project declaration and its managed installed artifacts. Make
+any customizations in the source before removing an installed copy you edited.
+
 ## Add Individual Skills
 
 Pass `owner/repo` directly to install all skills from that repo — no flags required:

docs/src/content/docs/docs/guides/plugins.mdx

@@ -194,6 +194,55 @@ client targeting.
 
 See the [CLI reference](/docs/reference/cli/#skill-add) for all source formats.
 
+## Updates and Local Customizations
+
+For ordinary file installations, the declared plugin or skill source is the
+source of truth. Client directories such as `.agents/skills/`,
+`.claude/skills/`, and `.codex/skills/` contain installed copies. An update can
+replace edits made directly to those copies without a local-edit confirmation;
+uninstall can remove modified copies that AllAgents previously installed.
+
+Keep lasting customizations in a local source directory or a fork, then point
+the plugin declaration at that source. Edit the source files and run
+`allagents update` to sync them to the selected clients. See
+[Git remotes for file installations](#git-remotes-for-file-installations) for
+remote source formats. Native installs use the selected client's own plugin
+lifecycle; named profiles have separate
+[modified-resource protections](/docs/reference/cli/#profile).
+
+### Track configuration and optional snapshots in Git
+
+Commit `.allagents/workspace.yaml` in the project's Git repository so the team
+shares source declarations and client selections. AllAgents keeps its local
+`.allagents/sync-state.json` out of Git.
+
+You can also commit snapshots of installed project skills for review and
+recovery. Use the directory for your selected client; `.agents/skills/` is one
+possible destination, not the destination for every client. For a project that
+uses `.agents/skills/`:
+
+```bash
+git add .allagents/workspace.yaml .agents/skills/
+git commit -m "Track agent setup and installed skills"
+```
+
+Use the project's existing repository; a separate repository inside `.agents/`
+is not required. If the installed directory is ignored, keep that policy and
+version the source instead. A symlink committed to Git records its link target,
+not a snapshot of the linked files.
+
+Git can recover committed, tracked content after an update. For example, to
+inspect changes and restore the last committed project skill snapshot:
+
+```bash
+git diff -- .agents/skills/
+git restore --source=HEAD -- .agents/skills/
+```
+
+Restoring returns those files to the committed snapshot. Git does not prevent
+AllAgents from replacing working files, and it cannot recover edits that were
+never committed or files outside the repository, such as user-global installs.
+
 ## Disabling Individual Skills
 
 You can disable specific skills from a plugin without uninstalling the entire plugin: