Fix evolution run skills root alignment

crates/skilllite-agent/src/skills/mod.rs

@@ -41,7 +41,7 @@ pub struct LoadedSkill {
 /// Load skills from directories, parse SKILL.md, generate tool definitions.
 /// Also loads evolved skills from `_evolved/` subdirectories (EVO-4),
 /// skipping archived ones based on `.meta.json`.
-/// Skills are project-level only: evolution writes to workspace/.skills/_evolved/.
+/// Skills are project-level only: evolution writes under the effective workspace skills root.
 pub fn load_skills(skill_dirs: &[String]) -> Vec<LoadedSkill> {
     let mut skills = Vec::new();
 

crates/skilllite-assistant/src/i18n/messages/en.ts

@@ -278,7 +278,7 @@ export const enMessages: Record<string, string> = {
   "evolution.detail.reviewNoJudgement":
     "No system judgement yet (last evolution decision missing or empty).",
   "evolution.detail.reviewPendingEmpty":
-    "No pending skills. Newly evolved skills appear under .skills/_evolved/_pending/.",
+    "No pending skills. Newly evolved skills appear under skills/_evolved/_pending/ or legacy .skills/_evolved/_pending/.",
   "evolution.diff.sectionTitleEvolution": "Evolution",
   "evolution.diff.sectionTitleRest": " prompt diff",
   "evolution.diff.evolvedBadge": "✨ Evolved this run",

crates/skilllite-assistant/src/i18n/messages/zh.ts

@@ -264,7 +264,7 @@ export const zhMessages: Record<string, string> = {
   "evolution.detail.reviewPendingRefresh": "刷新列表",
   "evolution.detail.reviewNoJudgement": "暂无系统审核结论（最近一次进化判断未记录或为空）。",
   "evolution.detail.reviewPendingEmpty":
-    "暂无待确认技能。进化生成的新技能会出现在 .skills/_evolved/_pending/。",
+    "暂无待确认技能。进化生成的新技能会出现在 skills/_evolved/_pending/，或旧版 .skills/_evolved/_pending/。",
   "evolution.diff.sectionTitleEvolution": "进化",
   "evolution.diff.sectionTitleRest": "变更对比",
   "evolution.diff.evolvedBadge": "✨ 本轮已进化",

crates/skilllite-commands/src/evolution.rs

@@ -31,7 +31,8 @@ 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, then applies the shared
+/// `skills/` default with `.skills/` legacy fallback policy.
 fn resolve_skills_root(workspace: Option<&str>) -> Option<PathBuf> {
     let ws: PathBuf = workspace
         .filter(|s| !s.is_empty())
@@ -47,7 +48,10 @@ fn resolve_skills_root(workspace: Option<&str>) -> Option<PathBuf> {
     } else {
         std::env::current_dir().ok()?.join(ws)
     };
-    Some(ws.join(".skills"))
+    Some(
+        skilllite_core::skill::discovery::resolve_skills_dir_with_legacy_fallback(&ws, "skills")
+            .effective_path,
+    )
 }
 
 #[derive(Debug)]
@@ -1013,6 +1017,32 @@ pub fn cmd_repair_skills(skills_filter: Option<Vec<String>>, from_source: bool)
 mod tests {
     use super::*;
 
+    #[test]
+    fn resolve_skills_root_prefers_default_skills_dir_when_present() {
+        let tmp = tempfile::tempdir().expect("temp workspace");
+        let default_skills = tmp.path().join("skills");
+        let legacy_skills = tmp.path().join(".skills");
+        std::fs::create_dir_all(&default_skills).expect("create skills");
+        std::fs::create_dir_all(&legacy_skills).expect("create legacy skills");
+
+        let resolved = resolve_skills_root(Some(tmp.path().to_string_lossy().as_ref()))
+            .expect("resolve skills root");
+
+        assert_eq!(resolved, default_skills);
+    }
+
+    #[test]
+    fn resolve_skills_root_falls_back_to_legacy_skills_dir() {
+        let tmp = tempfile::tempdir().expect("temp workspace");
+        let legacy_skills = tmp.path().join(".skills");
+        std::fs::create_dir_all(&legacy_skills).expect("create legacy skills");
+
+        let resolved = resolve_skills_root(Some(tmp.path().to_string_lossy().as_ref()))
+            .expect("resolve skills root");
+
+        assert_eq!(resolved, legacy_skills);
+    }
+
     #[test]
     fn normalize_filters_validate_allowed_values() {
         assert_eq!(

crates/skilllite-evolution/src/run.rs

@@ -37,7 +37,7 @@ fn try_log_evolution_run_outcome(chat_root: &Path, reason: &str) {
 ///
 /// Returns [EvolutionRunResult]: SkippedBusy if another run in progress, NoScope if nothing to evolve, Completed(txn_id) otherwise.
 /// When force=true (manual trigger), bypass decision thresholds.
-/// skills_root: project-level dir (workspace/.skills). When None, skips skill evolution.
+/// skills_root: effective project-level skills root. When None, skips skill evolution.
 pub async fn run_evolution<L: EvolutionLlm>(
     chat_root: &Path,
     skills_root: Option<&Path>,

crates/skilllite-evolution/src/skill_synth/mod.rs

@@ -12,7 +12,7 @@
 //! - **Retry**: 任何 LLM 输出 JSON 解析失败时，将错误反馈给大模型并重试 1 次
 //! - 代码修改/修复仅由大模型完成，不使用正则或模式匹配
 //!
-//! All evolved skills live in `chat/skills/_evolved/` with `.meta.json` metadata.
+//! All evolved skills live under `<skills-root>/_evolved/` with `.meta.json` metadata.
 //! A10: Newly generated skills go to `_evolved/_pending/` until user confirms.
 
 mod env_helper;

tasks/TASK-2026-069-evolution-run-skills-root/CONTEXT.md

@@ -0,0 +1,41 @@
+# 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:
+  - `evolution_desktop::resolve_skills_root` uses `resolve_skills_dir_with_legacy_fallback(&root, "skills")`.
+  - `evolution_status` counts pending skills from the same effective skills root.
+  - `evolution::cmd_run` now uses the same `skills/` default with `.skills/` legacy fallback policy.
+  - When `skills/` exists, generated pending skills and desktop pending/status/confirm operations target the same root.
+
+## Architecture Fit
+
+- Layer boundaries involved:
+  - CLI entry crate dispatches to `skilllite-commands`.
+  - `skilllite-commands` may call lower-layer `skilllite-core` discovery helpers.
+- Interfaces to preserve:
+  - Existing `evolution run` CLI flags and JSON response shape.
+  - Existing legacy `.skills` fallback behavior for projects without `skills/`.
+
+## Dependency and Compatibility
+
+- New dependencies: none.
+- Backward compatibility notes:
+  - Existing projects with only `.skills/` continue to use `.skills/`.
+  - Projects with `skills/` get consistent behavior across run/pending/status/confirm.
+
+## Design Decisions
+
+- Decision: Update `evolution.rs` root resolution to call the same discovery helper used by desktop reads.
+  - Rationale: Reuses the established project skills-root policy and avoids duplicating fallback rules.
+  - Alternatives considered: Change desktop pending/status/confirm back to `.skills` only.
+  - Why rejected: That would undo the newer `skills/` default and break current `skilllite init` style workspaces.
+
+## Open Questions
+
+- [ ] Whether assistant background authorize should pass `--workspace` to `evolution run`; tracked as residual risk outside this minimal skills-root fix.

tasks/TASK-2026-069-evolution-run-skills-root/PRD.md

@@ -0,0 +1,37 @@
+# PRD
+
+## Background
+
+The recent desktop L2 evolution bridge delegates pending/status/confirm operations to CLI JSON commands. Those read pending evolved skills from the effective workspace skills directory, preferring `skills/` and falling back to `.skills/` only for legacy workspaces. The evolution run command still writes generated pending skills under `.skills/`, creating a split-brain path when `skills/` exists.
+
+## Objective
+
+Ensure evolution-generated pending skills are written to the same effective skills root that desktop pending/status/confirm operations read.
+
+## Functional Requirements
+
+- FR-1: `skilllite evolution run --workspace <ws>` must resolve its skills root with the shared `skills/` plus legacy fallback policy.
+- FR-2: `.skills`-only workspaces must remain compatible.
+- FR-3: Regression tests must prove both root-selection cases.
+
+## Non-Functional Requirements
+
+- Security: No new path traversal or permission bypass behavior.
+- Performance: No measurable impact; root resolution is local path checking only.
+- Compatibility: Preserve `.skills` fallback for existing legacy projects.
+
+## Constraints
+
+- Technical: Keep the fix in command-layer Rust code and reuse existing lower-layer discovery helpers.
+- Timeline: N/A for autonomous execution.
+
+## Success Metrics
+
+- Metric: Root selected by `evolution run` matches desktop pending/status root.
+- Baseline: Workspaces with `skills/` present write pending skills under `.skills`.
+- Target: Workspaces with `skills/` present write pending skills under `skills`, while `.skills`-only workspaces still use `.skills`.
+
+## Rollout
+
+- Rollout plan: Ship as a narrow bug fix with command-level regression tests.
+- Rollback plan: Revert the command helper change and tests if unexpected compatibility issues appear.

tasks/TASK-2026-069-evolution-run-skills-root/REVIEW.md

@@ -0,0 +1,55 @@
+# Review Report
+
+## Scope Reviewed
+
+- Files/modules:
+  - `crates/skilllite-commands/src/evolution.rs`
+  - `crates/skilllite-agent/src/skills/mod.rs`
+  - `crates/skilllite-evolution/src/run.rs`
+  - `crates/skilllite-evolution/src/skill_synth/mod.rs`
+  - `crates/skilllite-assistant/src/i18n/messages/en.ts`
+  - `crates/skilllite-assistant/src/i18n/messages/zh.ts`
+  - `tasks/TASK-2026-069-evolution-run-skills-root/*`
+  - `tasks/board.md`
+- Commits/changes:
+  - Aligned `evolution run` skills-root resolution with the shared `skills/` plus legacy `.skills` fallback policy.
+  - Added focused unit regressions for default `skills/` preference and `.skills` fallback.
+  - Updated user-facing pending-empty messages and stale internal comments.
+
+## Findings
+
+- Critical: pre-fix path split made generated pending skills invisible/unconfirmable when a workspace had `skills/`.
+- Major: fixed by reusing the shared root-resolution helper in `evolution run`.
+- Minor: residual background authorize `--workspace` omission remains a separate follow-up risk outside this fix.
+
+## Quality Gates
+
+- Architecture boundary checks: `pass`
+- Security invariants: `pass`
+- Required tests executed: `pass`
+- Docs sync (EN/ZH): `pass`
+
+## Test Evidence
+
+- Commands run:
+  - `cargo fmt --check`
+  - `cargo test -p skilllite-commands --features agent resolve_skills_root`
+  - `cargo test -p skilllite-commands --features agent`
+  - `cargo test -p skilllite`
+  - `cargo clippy --all-targets -- -D warnings`
+  - `cargo test`
+  - `python3 scripts/validate_tasks.py`
+- Key outputs:
+  - Initial focused test attempt failed before running because Cargo 1.83 did not support edition 2024 dependency metadata; `rustup update stable && rustup default stable` updated to Rust/Cargo 1.96.
+  - Focused regressions: `2 passed; 0 failed`.
+  - `cargo test -p skilllite-commands --features agent`: `41 passed; 0 failed`.
+  - `cargo test -p skilllite`: integration/unit tests passed, including `20` skill management tests and `2` E2E minimal tests.
+  - `cargo clippy --all-targets -- -D warnings`: finished successfully.
+  - `cargo test`: full workspace passed; final suites included `skilllite-sandbox` `94 passed` and all doc-tests completed without failures.
+  - `python3 scripts/validate_tasks.py`: `Task validation passed (69 task directories checked).`
+
+## Decision
+
+- Merge readiness: `ready`
+- Follow-up actions:
+  - Consider a separate task for assistant authorize background run workspace argument and UI-only API key propagation.

tasks/TASK-2026-069-evolution-run-skills-root/STATUS.md

@@ -0,0 +1,21 @@
+# Status Journal
+
+## Timeline
+
+- 2026-06-17:
+  - Progress: Confirmed a concrete path split where `evolution run` writes pending skills under `.skills` while desktop pending/status/confirm read the effective `skills` root.
+  - Blockers: None.
+  - Next step: Done; fix, tests, review, and board update completed.
+- 2026-06-17:
+  - Progress: Updated `evolution run` skills-root resolution to use the shared `skills/` default with `.skills/` fallback policy; added focused unit regressions and synced user-facing pending-empty messages.
+  - Blockers: None.
+  - Next step: None.
+
+## 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-2026-069-evolution-run-skills-root/TASK.md

@@ -0,0 +1,73 @@
+# TASK Card
+
+## Metadata
+
+- Task ID: `TASK-2026-069`
+- Title: Evolution run skills-root alignment
+- Status: `done`
+- Priority: `P0`
+- Owner: `agent`
+- Contributors:
+- Created: `2026-06-17`
+- Target milestone:
+
+## Problem
+
+Recent L2 evolution bridge work made desktop pending/status/confirm paths resolve the effective workspace skills directory as `skills/` with legacy fallback to `.skills/`. The synchronous `skilllite evolution run` path still hardcodes `workspace/.skills`. In a workspace where `skills/` exists, evolution can generate pending skills under `.skills/_evolved/_pending` while desktop UI reads `skills/_evolved/_pending`, making generated skills invisible and unconfirmable.
+
+## Scope
+
+- In scope:
+  - Align `skilllite evolution run` skills-root resolution with desktop pending/status/confirm paths.
+  - Add focused regression coverage proving workspaces with `skills/` present use `skills/_evolved`.
+  - Keep the legacy `.skills` fallback when `skills/` is absent.
+- Out of scope:
+  - Broad evolution run architecture changes.
+  - Changing pending skill file formats or evolution DB schema.
+  - Reworking assistant background process API key handling.
+
+## Acceptance Criteria
+
+- [x] `evolution run` resolves the same effective skills root as pending/status/confirm for explicit workspaces.
+- [x] Regression tests cover `skills/` preference and `.skills` legacy fallback.
+- [x] Required Rust and task validation commands pass.
+
+## Risks
+
+- Risk: Changing the evolution run write root could surprise legacy workspaces.
+  - Impact: Existing `.skills`-only workspaces must keep working.
+  - Mitigation: Use the existing `resolve_skills_dir_with_legacy_fallback` helper so `.skills` remains selected only when `skills/` is absent.
+- Risk: Over-widening path semantics.
+  - Impact: Could change unrelated skill discovery behavior.
+  - Mitigation: Limit the fix to the command-layer skills root used by `evolution run`.
+
+## Validation Plan
+
+- Required tests:
+  - Unit regression tests in `skilllite-commands`.
+  - CLI/commands behavior tests required by policy.
+- Commands to run:
+  - `cargo fmt --check`
+  - `cargo clippy --all-targets -- -D warnings`
+  - `cargo test -p skilllite-commands --features agent`
+  - `cargo test -p skilllite`
+  - `cargo test`
+  - `python3 scripts/validate_tasks.py`
+- Manual checks:
+  - Inspect the changed files after edits.
+
+## Regression Scope
+
+- Areas likely affected:
+  - `skilllite evolution run`
+  - Desktop evolution manual trigger and post-authorize background run
+  - Pending evolved skill visibility and confirmation
+- Explicit non-goals:
+  - DB workspace default semantics when `--workspace` is omitted.
+  - Tauri UI copy or frontend state management.
+
+## Links
+
+- Source TODO section: daily critical bug-finding automation, 2026-06-17.
+- Related PRs/issues:
+- Related docs: `docs/en/ASSISTANT-SPLIT-ARCHITECTURE.md`, `docs/zh/ASSISTANT-SPLIT-ARCHITECTURE.md`

tasks/board.md

@@ -1,6 +1,6 @@
 # Task Board
 
-Last updated: 2026-06-10 (TASK-2026-068 evolution workspace db scope done)
+Last updated: 2026-06-17 (TASK-2026-069 evolution run skills-root alignment done)
 
 ## In Progress
 
@@ -17,6 +17,7 @@ Last updated: 2026-06-10 (TASK-2026-068 evolution workspace db scope done)
 
 ## Done
 
+- `TASK-2026-069-evolution-run-skills-root` - Status: `done` - Owner: `agent`
 - `TASK-2026-068-evolution-workspace-db-scope` - Status: `done` - Owner: `agent`
 - `TASK-2026-067-utf8-llm-error-truncate` - Status: `done` - Owner: `agent`
 - `TASK-2026-066-utf8-evolution-log-truncate` - Status: `done` - Owner: `agent`