Fix evolution pending skills root alignment

crates/skilllite-commands/src/evolution.rs

@@ -31,7 +31,7 @@ use skilllite_core::protocol::{NewSkill, NodeResult};
 use skilllite_core::skill::manifest;
 
 /// Resolve workspace for project-level skill evolution.
-/// Uses SKILLLITE_WORKSPACE env or current_dir. Returns workspace/.skills.
+/// Uses SKILLLITE_WORKSPACE env or current_dir. Returns the effective workspace skills root.
 fn resolve_skills_root(workspace: Option<&str>) -> Option<PathBuf> {
     let ws: PathBuf = workspace
         .filter(|s| !s.is_empty())
@@ -47,7 +47,12 @@ fn resolve_skills_root(workspace: Option<&str>) -> Option<PathBuf> {
     } else {
         std::env::current_dir().ok()?.join(ws)
     };
-    Some(ws.join(".skills"))
+    let resolution =
+        skilllite_core::skill::discovery::resolve_skills_dir_with_legacy_fallback(&ws, "skills");
+    if let Some(warning) = resolution.conflict_warning() {
+        eprintln!("{}", warning);
+    }
+    Some(resolution.effective_path)
 }
 
 #[derive(Debug)]
@@ -1030,6 +1035,33 @@ mod tests {
         assert!(normalize_risk_filter(Some("urgent")).is_err());
     }
 
+    #[test]
+    fn resolve_skills_root_prefers_default_skills_dir() {
+        let root =
+            std::env::temp_dir().join(format!("skilllite-evo-root-test-{}", uuid::Uuid::new_v4()));
+        std::fs::create_dir_all(root.join("skills")).expect("create skills dir");
+        std::fs::create_dir_all(root.join(".skills")).expect("create legacy skills dir");
+
+        let resolved =
+            resolve_skills_root(Some(root.to_str().expect("temp path utf8"))).expect("resolve");
+
+        assert_eq!(resolved, root.join("skills"));
+        let _ = std::fs::remove_dir_all(&root);
+    }
+
+    #[test]
+    fn resolve_skills_root_falls_back_to_legacy_skills_dir() {
+        let root =
+            std::env::temp_dir().join(format!("skilllite-evo-root-test-{}", uuid::Uuid::new_v4()));
+        std::fs::create_dir_all(root.join(".skills")).expect("create legacy skills dir");
+
+        let resolved =
+            resolve_skills_root(Some(root.to_str().expect("temp path utf8"))).expect("resolve");
+
+        assert_eq!(resolved, root.join(".skills"));
+        let _ = std::fs::remove_dir_all(&root);
+    }
+
     #[test]
     fn query_backlog_rows_applies_filters() {
         let root =

tasks/TASK-2026-067-evolution-skills-root-alignment/CONTEXT.md

@@ -0,0 +1,37 @@
+# Technical Context
+
+## Current State
+
+- Relevant crates/files:
+  - `crates/skilllite-commands/src/evolution.rs`
+  - `crates/skilllite-commands/src/evolution_desktop.rs`
+  - `crates/skilllite-commands/src/evolution_status.rs`
+  - `crates/skilllite-core/src/skill/discovery.rs`
+- Current behavior:
+  - Desktop pending/status/confirm paths use `resolve_skills_dir_with_legacy_fallback(workspace, "skills")`.
+  - `evolution run` and repair helper resolution return `workspace/.skills` directly.
+
+## Architecture Fit
+
+- Layer boundaries involved:
+  - `skilllite-commands` should call shared `skilllite-core` discovery helpers rather than duplicating root policy.
+- Interfaces to preserve:
+  - Existing CLI flags, JSON payloads, and legacy `.skills` fallback semantics.
+
+## Dependency and Compatibility
+
+- New dependencies: None.
+- Backward compatibility notes:
+  - `.skills` remains the effective root when `skills/` is absent.
+  - Workspaces with both roots follow the established default of preferring `skills/`.
+
+## Design Decisions
+
+- Decision: Reuse `skilllite_core::skill::discovery::resolve_skills_dir_with_legacy_fallback` for evolution skill root resolution.
+  - Rationale: It is already the shared policy for skill command and desktop evolution read paths.
+  - Alternatives considered: Change desktop pending/status/confirm back to `.skills`.
+  - Why rejected: That would diverge from current `skilllite init` default behavior and other command helpers.
+
+## Open Questions
+
+- [x] Is a docs update required? No user-facing command or documented default changes; the fix restores the current documented `skills/` default with `.skills` compatibility.

tasks/TASK-2026-067-evolution-skills-root-alignment/PRD.md

@@ -0,0 +1,41 @@
+# PRD
+
+## Background
+
+The desktop L2 JSON migration moved pending skill reads and confirmations through CLI helpers that
+resolve the effective skills directory as `skills/` with fallback to `.skills`. The evolution run
+command still resolves the skill generation root as `.skills` directly. This splits generated pending
+skills from the UI path in current default workspaces.
+
+## Objective
+
+Ensure all evolution skill write/read paths use one effective workspace skills root. Default
+workspaces should use `skills/`, while legacy `.skills`-only workspaces should continue to work.
+
+## Functional Requirements
+
+- FR-1: Resolve evolution skill roots through the shared `resolve_skills_dir_with_legacy_fallback` behavior.
+- FR-2: Preserve `.skills` fallback when `skills/` is absent.
+- FR-3: Keep existing CLI arguments and JSON output shapes unchanged.
+
+## Non-Functional Requirements
+
+- Security: Do not widen path access beyond the current workspace skills directory resolution.
+- Performance: Root resolution should remain local filesystem checks only.
+- Compatibility: Existing `.skills`-only workspaces must remain supported.
+
+## Constraints
+
+- Technical: Keep the fix localized to command-layer root selection and tests.
+- Timeline: N/A for autonomous execution.
+
+## Success Metrics
+
+- Metric: Pending skills generated by evolution are visible to the existing pending/status/confirm path.
+- Baseline: `evolution run` writes to `.skills` even when default `skills/` exists.
+- Target: `evolution run` uses `skills/` when present and `.skills` only as legacy fallback.
+
+## Rollout
+
+- Rollout plan: Ship as a minimal Rust command-layer fix with regression tests.
+- Rollback plan: Revert the command-layer resolver change if unexpected compatibility issues appear.

tasks/TASK-2026-067-evolution-skills-root-alignment/REVIEW.md

@@ -0,0 +1,47 @@
+# Review Report
+
+## Scope Reviewed
+
+- Files/modules:
+  - `crates/skilllite-commands/src/evolution.rs`
+  - `crates/skilllite-commands/src/evolution_desktop.rs`
+  - `crates/skilllite-commands/src/evolution_status.rs`
+  - `crates/skilllite-core/src/skill/discovery.rs`
+- Commits/changes:
+  - Recent desktop L2 JSON bridge changes around evolution pending/status/confirm.
+  - This fix aligns the evolution write-side root resolver with the existing read-side resolver.
+
+## Findings
+
+- Critical: None remaining in the patched path.
+- Major: Fixed root split where `evolution run` wrote pending skills to `.skills` while desktop pending/status/confirm read `skills/` in default workspaces.
+- Minor: Other investigated desktop bridge issues were left out of scope because they did not meet the critical bug bar for this run.
+
+## Quality Gates
+
+- Architecture boundary checks: `pass`
+- Security invariants: `pass`
+- Required tests executed: `pass`
+- Docs sync (EN/ZH): `pass` - no docs update required because the fix restores the current `skills/` default behavior and keeps CLI/API shape unchanged.
+
+## Test Evidence
+
+- Commands run:
+  - `rustup update stable && rustup default stable`
+  - `cargo test -p skilllite-commands --features agent resolve_skills_root`
+  - `cargo fmt --check`
+  - `cargo clippy --all-targets -- -D warnings`
+  - `cargo test`
+  - `cargo test -p skilllite`
+  - `python3 scripts/validate_tasks.py`
+- Key outputs:
+  - Focused regression: `2 passed; 0 failed`.
+  - Clippy: `Finished dev profile`.
+  - Full tests: `cargo test` completed successfully; regression tests listed as `evolution::tests::resolve_skills_root_* ... ok`.
+  - Package tests: `cargo test -p skilllite` completed successfully.
+  - Task validation: `Task validation passed (67 task directories checked).`
+
+## Decision
+
+- Merge readiness: `ready`
+- Follow-up actions: Continue separate investigation for lower-confidence desktop bridge UX issues if needed; not included in this critical bug fix.

tasks/TASK-2026-067-evolution-skills-root-alignment/STATUS.md

@@ -0,0 +1,21 @@
+# Status Journal
+
+## Timeline
+
+- 2026-05-30:
+  - Progress: Investigated recent desktop L2 evolution changes, confirmed a skills-root split between write and read paths, and implemented resolver alignment with regression tests.
+  - Blockers: None.
+  - Next step: Open PR and report results.
+- 2026-05-30:
+  - Progress: Validation passed: `cargo fmt --check`, `cargo clippy --all-targets -- -D warnings`, `cargo test`, `cargo test -p skilllite`, and `python3 scripts/validate_tasks.py`.
+  - Blockers: None.
+  - Next step: Done.
+
+## Checkpoints
+
+- [x] PRD drafted before implementation (or `N/A` recorded)
+- [x] Context drafted before implementation (or `N/A` recorded)
+- [x] Implementation complete
+- [x] Tests passed
+- [x] Review complete
+- [x] Board updated

tasks/TASK-2026-067-evolution-skills-root-alignment/TASK.md

@@ -0,0 +1,70 @@
+# TASK Card
+
+## Metadata
+
+- Task ID: `TASK-2026-067`
+- Title: Align evolution skills root
+- Status: `done`
+- Priority: `P1`
+- Owner: `agent`
+- Contributors:
+- Created: `2026-05-30`
+- Target milestone:
+
+## Problem
+
+Recent desktop evolution paths list, count, confirm, and reject pending skills through the current
+default `skills/` directory with legacy fallback to `.skills/`. The `evolution run` path still writes
+generated pending skills to `.skills` unconditionally, so default `skilllite init` workspaces that use
+`skills/` can generate pending skills that the desktop cannot see or confirm.
+
+## Scope
+
+- In scope:
+  - Align `evolution run` and related evolution skill operations with the shared `skills/` default plus `.skills` legacy fallback.
+  - Add focused regression tests for default and legacy root resolution.
+  - Validate Rust formatting, linting, tests, and task artifact shape.
+- Out of scope:
+  - Broad redesign of skill identity, duplicate skill handling, or desktop error presentation.
+  - Changing LLM evolution policy, backlog schema, or sandbox behavior.
+
+## Acceptance Criteria
+
+- [x] `evolution run` resolves the same effective skills root as desktop pending/status/confirm for default workspaces.
+- [x] Existing `.skills`-only workspaces remain supported.
+- [x] Regression tests cover default `skills/` and legacy `.skills` behavior.
+- [x] Required validation commands pass or any blocker is recorded with output.
+
+## Risks
+
+- Risk: Changing the write target may affect users with both `skills/` and `.skills/`.
+  - Impact: New evolved skills follow `skills/`, while older pending skills in `.skills` remain in the legacy tree.
+  - Mitigation: Match the already-shipped shared fallback behavior: prefer `skills/` when present and fall back only when it is absent.
+
+## Validation Plan
+
+- Required tests:
+  - Regression tests in `crates/skilllite-commands/src/evolution.rs`.
+  - Workspace Rust tests required by policy.
+- Commands to run:
+  - `cargo fmt --check` - passed
+  - `cargo clippy --all-targets -- -D warnings` - passed
+  - `cargo test` - passed
+  - `cargo test -p skilllite` - passed
+  - `python3 scripts/validate_tasks.py` - passed
+- Manual checks:
+  - Re-read modified files and task board after updates.
+
+## Regression Scope
+
+- Areas likely affected:
+  - CLI evolution skill generation, pending/confirm/reject, and repair skill root selection.
+  - Desktop evolution UI visibility of generated pending skills.
+- Explicit non-goals:
+  - No change to chat skill loading, skill import, or assistant frontend components.
+
+## Links
+
+- Source TODO section: N/A
+- Related PRs/issues: Recent `feat/runtime-skills-l2-json` and UTF-8 logging follow-up.
+- Related docs: `spec/docs-sync.md` reviewed; no docs change needed because the fix restores documented/current default behavior.

tasks/board.md

@@ -1,6 +1,6 @@
 # Task Board
 
-Last updated: 2026-05-29 (TASK-2026-066 utf8 evolution log truncate done)
+Last updated: 2026-05-30 (TASK-2026-067 evolution skills root alignment done)
 
 ## In Progress
 
@@ -17,6 +17,7 @@ Last updated: 2026-05-29 (TASK-2026-066 utf8 evolution log truncate done)
 
 ## Done
 
+- `TASK-2026-067-evolution-skills-root-alignment` - Status: `done` - Owner: `agent`
 - `TASK-2026-066-utf8-evolution-log-truncate` - Status: `done` - Owner: `agent`
 - `TASK-2026-064-env-keys-single-source` - Status: `done` - Owner: `agent`
 - `TASK-2026-063-extension-tool-metadata-dispatch` - Status: `done` - Owner: `agent`