fix: pi container repo mount target and npm update permissions

- Add Alembic migration to update built-in pi-agent manifest:
  * repo mount target from /workspace to ~/{{WORKSPACE_NAME}}
  * keep /workspace as compatibility symlink via working_dir
  * update startup chown target to $HOME/$WORKSPACE_NAME
- Pass REPO_NAME and WORKSPACE_NAME to compile_compose from instance_service
- Substitute {{WORKSPACE_NAME}} in manifest mount targets and expose it as
  a container env var so the entrypoint can create the /workspace symlink
- Generate entrypoint workspace symlink from runtime WORKSPACE_NAME env var
- Install npm_global packages into {home_dir}/.npm-global with PATH so the
  non-root container user can update global packages
- Update manifest compiler unit tests for the new behavior

Quality gates:
- pytest tests/unit: 207 passed
- ruff: clean on changed files
- mypy: clean on changed files
- alembic heads: single head

apps/api/alembic/versions/.pi-map.index.md

@@ -2,7 +2,7 @@
 dir: apps/api/alembic/versions
 
 ## role
-Database schema evolution and versioning management for the API application using Alembic migration scripts.
+Database schema version control and incremental migration management for the API application, tracking the evolution of tables supporting users, SSH keys, projects, git repositories, tool types/instances, config profiles, workspaces, monitoring, notifications, and terminal sessions.
 ## parent
 index: apps/api/alembic/.pi-map.index.md
 map: apps/api/alembic/.pi-map.md
@@ -49,6 +49,7 @@ map: apps/api/alembic/.pi-map.md
 - 2026_06_01_add_workspaces.py
 - 2026_06_13_make_clone_mode_nullable.py
 - 2026_06_14_104415_add_tool_type_home_directory.py
+- 2026_06_14_182955_fix_pi_agent_home_directory_mount.py
 - 398082499c30_add_tool_config_fields.py
 - 6fc7bfcf199f_merge_remove_is_builtin_and_add_config_.py
 - 86cec91fdb00_merge_profile_resolver_and_workspaces_.py