The Active Agents refresh loop could keep VS Code's Git SCM pointed at a deleted agent worktree. When a session worktree path no longer exists, the extension now asks Git to close that repository URI and removes a matching workspace folder once, while preserving watcher refresh for live sessions.

This also mirrors finish script/template parity so the metadata gate stays green after remote cleanup warning handling.

Constraint: VS Code Git can keep an already-open repository in SCM after the worktree path is deleted.

Rejected: Rely only on repositoryScanIgnoredFolders | it does not close repositories already opened in SCM.

Confidence: high

Scope-risk: moderate

Directive: Keep vscode/guardex-active-agents and templates/vscode/guardex-active-agents in sync for extension behavior changes.

Tested: node --test test/vscode-active-agents-session-state.test.js

Tested: node --test test/metadata.test.js

Tested: bash -n scripts/agent-branch-finish.sh

Tested: npm test (285 pass, 1 skipped)

Not-tested: Live VS Code window reload behavior after installing the updated extension.