The plugin loader already pruned stale registry entries, but stale enabled state
could linger in settings.json after bundled or installed plugin discovery
cleaned up missing installs. This change removes those orphaned enabled flags
when stale registry entries are dropped so loader-managed state stays coherent.
Constraint: Commit only plugin loader/registry code in this pass
Rejected: Leave stale enabled flags in settings.json | state drift would survive loader self-healing
Confidence: high
Scope-risk: narrow
Reversibility: clean
Directive: Any future loader-side pruning should remove matching enabled state in the same code path
Tested: cargo fmt --all; cargo test -p plugins
Not-tested: Interactive CLI /plugins flows against manually edited settings.json
Expanded the plugin manager so installed plugin discovery now falls back across
install-root scans and registry-only paths without breaking on stale entries.
Missing registry install paths are pruned during discovery, while valid
registry-backed installs outside the install root remain loadable.
Constraint: Keep the change isolated to plugin manifest/manager/registry code
Rejected: Fail listing when any registry install path is missing | stale local state should not block plugin discovery
Confidence: high
Scope-risk: narrow
Reversibility: clean
Directive: Discovery now self-heals missing registry install paths; preserve the registry-fallback path for valid installs outside install_root
Tested: cargo fmt --all; cargo test -p plugins
Not-tested: End-to-end CLI flows with mixed stale and git-backed installed plugins
Expanded the Rust plugin loader coverage around manifest parsing so invalid
permission values, invalid tool permissions, and multi-error manifests are
validated in a structured way. Added scan-path coverage for installed plugin
directories so both root and packaged manifests are discovered from the install
root, independent of registry entries.
Constraint: Keep plugin loader changes isolated to the plugins crate surface
Rejected: Add a new manifest crate for shared schemas | unnecessary scope for this pass
Confidence: high
Scope-risk: narrow
Reversibility: clean
Directive: If manifest permissions or tool permission labels expand, update both the enums and validation tests together
Tested: cargo fmt --all; cargo test -p plugins
Not-tested: Cross-crate runtime consumption of any future expanded manifest permission variants
