Document the new tools, plugins, skills, MCP panel, and item repair

Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)

Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>

docs/permissions.md

@@ -33,7 +33,8 @@ remain are the ones worth reading.
 | Tool | Matched against |
 |---|---|
 | `bash` | the command, e.g. `git status --porcelain` |
-| `read_file` `write_file` `edit_file` `multi_edit` `list_dir` | the path |
+| `read_file` `write_file` `edit_file` `multi_edit` `delete_file` `list_dir` | the path |
+| `move_file` | both ends; one match is enough |
 | `apply_patch` | every file marker path in the patch |
 | `web_fetch` | the URL |
 | `read_many_files` | every path in the batch; one match is enough |
@@ -98,7 +99,7 @@ With no `permission` config:
 | `glob` `grep` `list_dir` | `allow` |
 | the git tools | `allow` — they cannot mutate anything |
 | `task`, and every session tool | `allow` — they touch the agent's own state |
-| `write_file` `edit_file` `multi_edit` `apply_patch` `bash` `web_fetch` | `ask` |
+| `write_file` `edit_file` `multi_edit` `apply_patch` `move_file` `delete_file` `bash` `web_fetch` | `ask` |
 | anything else, including every `mcp__*` tool | `ask` |
 
 Credentials are denied on read rather than gated, because there is no recovery. A model that