Context

PR #6881 renames the .kilocode config directory to .kilo across the CLI and VS Code extension. During rollout we keep backward compatibility and temporary migration helpers so existing installs continue to work without manual intervention.

This issue tracks the cleanup work that should happen after GA, once the rename has been live long enough.

What changed in PR #6881

• New config directory: .kilo (project-level and global ~/.kilo)
• Backward compatibility: both .kilo and .kilocode are read; .kilo takes precedence
• New writes go to .kilo
• Agent Manager data is auto-migrated from .kilocode/ to .kilo/ at startup

Post-GA cleanup tasks

Documentation updates

Update remaining references to .kilocode as a directory to .kilo in:

1. User-facing guides and configuration docs
2. README / quickstart docs
3. Agent Manager docs
4. AGENTS.md and other internal docs that mention directory paths
5. Skills / rules / workflows / MCP path documentation
6. Global config docs (~/.kilocode/ -> ~/.kilo/)
7. Release / migration notes that explain the rename and backward compatibility

Temporary code cleanup

Remove the temporary legacy .kilocode -> .kilo migration code added for the Agent Manager rollout, including:

• the migration helpers in packages/kilo-vscode/src/agent-manager/constants.ts
• any legacy Agent Manager ignore entries that are only kept to support that migration in packages/kilo-vscode/src/agent-manager/WorktreeManager.ts
• the related TODO that points back to this issue once the cleanup lands

What should NOT change

• .kilocodeignore, .kilocoderules, .kilocodemodes
• kilocode.kilo-code
• API property names like kilocodeToken and kilocodeOrganizationId

Timing

Do this after the GA release, when the rollout window for the .kilo rename and Agent Manager migration has passed.