[codex] Add clean command for managed tools

[halkn]

Summary

• Add ptm clean [--apply] for removing ptm-managed release tools that are no longer configured.
• Move release installs under ${XDG_DATA_HOME:-~/.local/share}/ptm/tools/<bin>/current and publish $XDG_BIN_HOME entries as symlinks.
• Remove opt_dir support; full archive extraction is now driven by bin_path_in_archive / extra_bins.
• Add per-tool .ptm.json metadata for managed release installs.

Breaking Changes / Migration Notes

• opt_dir is no longer a supported config field and is ignored by config loading.
• Release tools are no longer installed directly into $XDG_BIN_HOME; they are stored under the ptm managed root and exposed through symlinks.
• Existing release tools installed before this layout are not automatically adopted. They become managed after reinstall/update.
• ptm clean --apply removes only directories under the ptm managed root and symlinks that point into those directories.

npm / Bun Follow-up

ptm clean currently manages release-tool directories only. The CLI shape should support npm/bun later, but the internal clean plan will need to grow beyond tool_dir deletion to model package-manager uninstall actions.

Validation

• uv run pytest passed: 164 tests
• uv run ruff check src tests passed
• uv run ruff format --check src tests passed
• uv run ty check src tests passed