feat: implement repository clone mode with SSH key support

- Add clone_mode and branch fields to tool_instances
- Add ssh_key_id to git_repositories for per-repo SSH key assignment
- Implement host-side git cloning with branch selection (default: main)
- Mount SSH keys into containers for git operations in clone mode
- Add dirty state check on clone-mode instance deletion with confirmation
- Update SessionsPage with mount/clone selector, branch input, SSH key display
- Add SSH key selector to repository creation form
- Add dirty delete confirmation modal with changed files list
- Update API schemas and endpoints for new fields
- Sync delta specs to main specs (git-repo, tool-instances, repo-clone-mode)
- Archive completed OpenSpec change: repo-clone-mode-with-ssh
- Document git requirement for custom tool types

Quality gates: Frontend typecheck and build passed
OpenSpec: repo-clone-mode-with-ssh archived with all tasks complete

apps/web/src/router.tsx

@@ -14,8 +14,6 @@ import { SettingsPage, GeneralSettingsTab } from "./pages/settings";
 import { TerminalPage } from "./pages/terminal";
 import { ToolWorkshopPage } from "./pages/tool-workshop";
 import { SSHKeysPage } from "./pages/ssh-keys";
-import { ToolConfigsPage } from "./pages/tool-configs";
-import { ToolTypesPage } from "./pages/tool-types";
 import { SessionsPage } from "./pages/sessions";
 
 export const AppRouter = () => {
@@ -23,8 +21,6 @@ export const AppRouter = () => {
     <Routes>
       <Route path="/login" element={<LoginRedirectPage />} />
       <Route path="/ssh-keys" element={<Navigate to="/settings/ssh-keys" replace />} />
-      <Route path="/tool-types" element={<Navigate to="/settings/tool-types" replace />} />
-      <Route path="/tool-configs" element={<Navigate to="/settings/tool-configs" replace />} />
       <Route
         path="/"
         element={
@@ -44,8 +40,6 @@ export const AppRouter = () => {
           <Route index element={<Navigate to="general" replace />} />
           <Route path="general" element={<GeneralSettingsTab />} />
           <Route path="ssh-keys" element={<SSHKeysPage />} />
-          <Route path="tool-types" element={<ToolTypesPage />} />
-          <Route path="tool-configs" element={<ToolConfigsPage />} />
           <Route path="*" element={<Navigate to="general" replace />} />
         </Route>
         <Route path="sessions" element={<SessionsPage />} />