fix(core): address review findings F1-F4 + add 10 missing tests

F1: Add depth limit (max 5) to find_note_by_name and
    collect_obsidian_matches to prevent stack overflow on large vaults
F2: Fix bus_enqueue to use store_path parent instead of cwd
F3: Fix update_skill_md_from_patterns to preserve sections after
    the auto-generated marker instead of truncating them
F4: Fix extract_wikilinks to consume chars after | in [[Note|Display]]
    so subsequent links parse correctly

Tests added:
- extract_wikilinks: basic, display text, empty/broken
- find_note_by_name: depth limit enforcement
- resolve_wikilink: direct, nested, non-existent
- build_rejection_section: empty, sorted by count desc
- update_skill_md_from_patterns: append, replace preserving following sections

955 tests GREEN, clippy zero.

Closes #109

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

crates/miyabi-cli/src/main.rs

@@ -1301,7 +1301,7 @@ fn handle_gate_command(
                         println!("registered: {} ({})", task.id, task.title);
                     }
                     if !no_bus {
-                        bus_enqueue(&task.id, &task_title);
+                        bus_enqueue(&task.id, &task_title, store_path);
                     }
                 })
         }
@@ -2454,12 +2454,15 @@ fn truncate_str(s: &str, max_len: usize) -> String {
     }
 }
 
-fn bus_enqueue(task_id: &str, title: &str) {
-    let skill_runs_path = std::env::current_dir()
-        .ok()
-        .map(|cwd| cwd.join("skills/self-improving-skills/skill-runs.jsonl"));
+fn bus_enqueue(task_id: &str, title: &str, store_path: &std::path::Path) {
+    // Derive repo root from store_path (e.g. project_memory/tasks.json -> repo root)
+    let repo_root = store_path
+        .parent()
+        .and_then(|pm| pm.parent())
+        .unwrap_or(std::path::Path::new("."));
+    let skill_runs_path = repo_root.join("skills/self-improving-skills/skill-runs.jsonl");
 
-    if let Some(path) = skill_runs_path.filter(|p| p.parent().is_some_and(|d| d.exists())) {
+    if let Some(path) = Some(skill_runs_path).filter(|p| p.parent().is_some_and(|d| d.exists())) {
         let entry = serde_json::json!({
             "ts": chrono::Utc::now().to_rfc3339(),
             "agent": std::env::var("POLARIS_AGENT_ID").unwrap_or_else(|_| "system".into()),

crates/miyabi-core/src/dream.rs

@@ -161,29 +161,35 @@ fn update_skill_md_from_patterns(report: &DreamReport, repo_root: &Path) -> Resu
 
     let existing = fs::read_to_string(&skill_path)?;
     let marker = "## よくある拒否パターン（自動生成）";
-    if existing.contains(marker) {
-        // Already has auto-generated section — remove it for refresh
-        let before = existing.split(marker).next().unwrap_or(&existing);
-        let mut content = before.trim_end().to_string();
+    let new_section = build_rejection_section(&report.patterns.gate_rejections);
+
+    let content = if let Some(start_idx) = existing.find(marker) {
+        // Replace only the auto-generated section, preserving content after it
+        let after_marker = &existing[start_idx + marker.len()..];
+        // Find the next ## heading (or EOF) to determine section boundary
+        let section_end = after_marker
+            .find("\n## ")
+            .map(|i| start_idx + marker.len() + i + 1) // +1 to keep the newline before next heading
+            .unwrap_or(existing.len());
+        let mut content = existing[..start_idx].trim_end().to_string();
         content.push_str("\n\n");
-        content.push_str(&build_rejection_section(&report.patterns.gate_rejections));
-        content.push('\n');
-        let tmp = skill_path.with_extension("md.tmp");
-        fs::write(&tmp, &content)?;
-        fs::rename(&tmp, &skill_path)?;
+        content.push_str(&new_section);
+        content.push_str(&existing[section_end..]);
+        content
     } else {
         let mut content = existing;
         if !content.ends_with('\n') {
             content.push('\n');
         }
         content.push('\n');
-        content.push_str(&build_rejection_section(&report.patterns.gate_rejections));
+        content.push_str(&new_section);
         content.push('\n');
-        let tmp = skill_path.with_extension("md.tmp");
-        fs::write(&tmp, &content)?;
-        fs::rename(&tmp, &skill_path)?;
-    }
+        content
+    };
 
+    let tmp = skill_path.with_extension("md.tmp");
+    fs::write(&tmp, &content)?;
+    fs::rename(&tmp, &skill_path)?;
     Ok(())
 }
 
@@ -638,4 +644,93 @@ mod tests {
                     && args.first() == Some(&"commit".to_string()))
         );
     }
+
+    #[test]
+    fn build_rejection_section_empty() {
+        let section = build_rejection_section(&HashMap::new());
+        assert!(section.contains("| GATE | 回数 | 対処法 |"));
+        // heading + blank + table header + separator = 4 lines, no data rows
+        assert_eq!(section.lines().count(), 4);
+    }
+
+    #[test]
+    fn build_rejection_section_sorted_by_count_desc() {
+        let mut rejections = HashMap::new();
+        rejections.insert("GATE 0".to_string(), 1);
+        rejections.insert("GATE 3".to_string(), 5);
+        rejections.insert("GATE 4".to_string(), 3);
+
+        let section = build_rejection_section(&rejections);
+        let lines: Vec<&str> = section.lines().collect();
+        // lines: [0]=heading, [1]=blank, [2]=table header, [3]=separator, [4..]=data
+        assert!(lines[4].contains("GATE 3"));
+        assert!(lines[4].contains("5"));
+        assert!(lines[5].contains("GATE 4"));
+        assert!(lines[6].contains("GATE 0"));
+    }
+
+    #[test]
+    fn update_skill_md_appends_when_no_marker() {
+        let tmp = TempDir::new().unwrap();
+        let skills_dir = tmp.path().join("skills/polaris-ops");
+        fs::create_dir_all(&skills_dir).unwrap();
+        let skill_path = skills_dir.join("SKILL.md");
+        fs::write(&skill_path, "# Polaris Ops\n\nExisting content.\n").unwrap();
+
+        let mut rejections = HashMap::new();
+        rejections.insert("GATE 3".to_string(), 2);
+        let report = DreamReport {
+            patterns: DreamPatterns {
+                gate_rejections: rejections,
+                ..Default::default()
+            },
+            learnings: Vec::new(),
+            events_processed: 0,
+        };
+
+        update_skill_md_from_patterns(&report, tmp.path()).unwrap();
+        let content = fs::read_to_string(&skill_path).unwrap();
+        assert!(content.contains("# Polaris Ops"));
+        assert!(content.contains("Existing content."));
+        assert!(content.contains("## よくある拒否パターン（自動生成）"));
+        assert!(content.contains("GATE 3"));
+    }
+
+    #[test]
+    fn update_skill_md_replaces_marker_preserves_following_sections() {
+        let tmp = TempDir::new().unwrap();
+        let skills_dir = tmp.path().join("skills/polaris-ops");
+        fs::create_dir_all(&skills_dir).unwrap();
+        let skill_path = skills_dir.join("SKILL.md");
+        fs::write(
+            &skill_path,
+            "# Polaris Ops\n\n\
+             ## よくある拒否パターン（自動生成）\n\n\
+             | GATE | 回数 | 対処法 |\n|------|------|--------|\n| old | 1 | old |\n\n\
+             ## 関連スキル\n\n- important link\n",
+        )
+        .unwrap();
+
+        let mut rejections = HashMap::new();
+        rejections.insert("GATE 4".to_string(), 7);
+        let report = DreamReport {
+            patterns: DreamPatterns {
+                gate_rejections: rejections,
+                ..Default::default()
+            },
+            learnings: Vec::new(),
+            events_processed: 0,
+        };
+
+        update_skill_md_from_patterns(&report, tmp.path()).unwrap();
+        let content = fs::read_to_string(&skill_path).unwrap();
+        // Old data should be gone
+        assert!(!content.contains("| old |"));
+        // New data should be present
+        assert!(content.contains("GATE 4"));
+        assert!(content.contains("7"));
+        // Following section MUST be preserved
+        assert!(content.contains("## 関連スキル"));
+        assert!(content.contains("- important link"));
+    }
 }

crates/miyabi-core/src/protocol.rs

@@ -507,6 +507,7 @@ impl DeterministicExecutionProtocol {
             |task| {
                 let from = task.current_state;
                 task.current_state = TaskState::Done;
+                task.completion_mode = CompletionMode::Manual;
                 Ok(serde_json::json!({
                     "from": from,
                     "to": TaskState::Done,
@@ -1452,7 +1453,7 @@ fn find_obsidian_notes(
     }
 
     let mut matches = Vec::new();
-    collect_obsidian_matches(vault_path, &keywords, &mut matches)?;
+    collect_obsidian_matches(vault_path, &keywords, &mut matches, MAX_VAULT_DEPTH)?;
     matches.sort_by(|left, right| {
         right
             .0
@@ -1467,12 +1468,16 @@ fn collect_obsidian_matches(
     directory: &Path,
     keywords: &[String],
     matches: &mut Vec<(usize, PathBuf)>,
+    depth: usize,
 ) -> Result<(), Error> {
+    if depth == 0 {
+        return Ok(());
+    }
     for entry in fs::read_dir(directory)? {
         let entry = entry?;
         let path = entry.path();
         if path.is_dir() {
-            collect_obsidian_matches(&path, keywords, matches)?;
+            collect_obsidian_matches(&path, keywords, matches, depth - 1)?;
             continue;
         }
         if path.extension().and_then(|ext| ext.to_str()) != Some("md") {
@@ -1509,6 +1514,12 @@ fn extract_wikilinks(content: &str) -> Vec<String> {
                 }
                 if inner == '|' {
                     // [[Note|Display]] — take the note part before |
+                    // consume remaining chars until ']' so parser stays aligned
+                    for remaining in chars.by_ref() {
+                        if remaining == ']' {
+                            break;
+                        }
+                    }
                     break;
                 }
                 name.push(inner);
@@ -1522,23 +1533,28 @@ fn extract_wikilinks(content: &str) -> Vec<String> {
     links
 }
 
+const MAX_VAULT_DEPTH: usize = 5;
+
 fn resolve_wikilink(vault_path: &Path, link_name: &str) -> Option<PathBuf> {
     // Try exact match first
     let exact = vault_path.join(format!("{link_name}.md"));
     if exact.exists() {
         return Some(exact);
     }
-    // Search recursively for the note
-    find_note_by_name(vault_path, link_name)
+    // Search recursively for the note (depth-limited)
+    find_note_by_name(vault_path, link_name, MAX_VAULT_DEPTH)
 }
 
-fn find_note_by_name(directory: &Path, name: &str) -> Option<PathBuf> {
+fn find_note_by_name(directory: &Path, name: &str, depth: usize) -> Option<PathBuf> {
+    if depth == 0 {
+        return None;
+    }
     let target = format!("{}.md", name.to_ascii_lowercase());
     for entry in fs::read_dir(directory).ok()? {
         let entry = entry.ok()?;
         let path = entry.path();
         if path.is_dir() {
-            if let Some(found) = find_note_by_name(&path, name) {
+            if let Some(found) = find_note_by_name(&path, name, depth - 1) {
                 return Some(found);
             }
         } else if path
@@ -2617,6 +2633,73 @@ mod tests {
             .unwrap();
 
         assert_eq!(task.current_state, TaskState::Done);
+        assert_eq!(task.completion_mode, CompletionMode::Manual);
+    }
+
+    #[test]
+    fn full_lifecycle_register_to_merged_releases_lock() {
+        let (_tmp, protocol) = fixture();
+        protocol
+            .register(
+                RegisterTaskRequest {
+                    issue: 1,
+                    task_id: "e2e-lifecycle".into(),
+                    title: "E2E lifecycle".into(),
+                    dependencies: vec![],
+                    soft_dependencies: vec![],
+                    priority: 0,
+                    completion_mode: CompletionMode::GithubPr,
+                },
+                "test-agent",
+                "test-node",
+            )
+            .unwrap();
+        protocol
+            .record_impact(
+                "e2e-lifecycle",
+                ImpactInput {
+                    risk_level: ImpactRiskLevel::Low,
+                    affected_symbols: 1,
+                    depth1: vec!["e2e".into()],
+                    analyzed_commit: None,
+                    input_hash: None,
+                    approve: false,
+                },
+                "test-agent",
+                "test-node",
+            )
+            .unwrap();
+        protocol
+            .assign(
+                "e2e-lifecycle",
+                "test-agent",
+                "test-node",
+                &[String::from("src/test.rs")],
+            )
+            .unwrap();
+        protocol
+            .record_branch(
+                "e2e-lifecycle",
+                "feature/issue-1-test",
+                "test-agent",
+                "test-node",
+            )
+            .unwrap();
+        protocol
+            .record_pr("e2e-lifecycle", 42, "test-agent", "test-node")
+            .unwrap();
+        let merged = protocol
+            .record_merge(
+                "e2e-lifecycle",
+                "0123456789abcdef0123456789abcdef01234567",
+                "test-agent",
+                "test-node",
+            )
+            .unwrap();
+
+        assert_eq!(merged.current_state, TaskState::Merged);
+        assert!(merged.lock.is_none());
+        assert!(protocol.locks().unwrap().is_empty());
     }
 
     #[test]
@@ -2671,4 +2754,66 @@ mod tests {
         };
         assert!(after_heartbeat > before_heartbeat);
     }
+
+    #[test]
+    fn extract_wikilinks_basic() {
+        assert_eq!(
+            extract_wikilinks("See [[Note A]] and [[Note B]]"),
+            vec!["Note A", "Note B"]
+        );
+    }
+
+    #[test]
+    fn extract_wikilinks_with_display_text() {
+        // After fixing F4, [[A|B]] should yield "A" and not corrupt next link
+        assert_eq!(
+            extract_wikilinks("[[Foo|display text]] then [[Bar]]"),
+            vec!["Foo", "Bar"]
+        );
+    }
+
+    #[test]
+    fn extract_wikilinks_empty_and_broken() {
+        assert!(extract_wikilinks("no links here").is_empty());
+        assert!(extract_wikilinks("[[]]").is_empty()); // empty name
+        assert!(extract_wikilinks("[[ ]]").is_empty()); // whitespace only
+        // Unclosed link: should still extract the name
+        assert_eq!(extract_wikilinks("[[unclosed"), vec!["unclosed"]);
+    }
+
+    #[test]
+    fn find_note_by_name_respects_depth_limit() {
+        let tmp = TempDir::new().unwrap();
+        // Create a deeply nested note: a/b/c/d/e/f/g/note.md
+        let deep_dir = tmp.path().join("a/b/c/d/e/f/g");
+        fs::create_dir_all(&deep_dir).unwrap();
+        fs::write(deep_dir.join("target.md"), "deep note").unwrap();
+
+        // depth=5 should NOT find it (7 levels deep)
+        assert!(find_note_by_name(tmp.path(), "target", 5).is_none());
+
+        // depth=8 should find it
+        assert!(find_note_by_name(tmp.path(), "target", 8).is_some());
+
+        // depth=0 always returns None
+        assert!(find_note_by_name(tmp.path(), "target", 0).is_none());
+    }
+
+    #[test]
+    fn resolve_wikilink_finds_direct_and_nested() {
+        let tmp = TempDir::new().unwrap();
+
+        // Direct file
+        fs::write(tmp.path().join("Direct.md"), "content").unwrap();
+        assert!(resolve_wikilink(tmp.path(), "Direct").is_some());
+
+        // Nested file
+        let sub = tmp.path().join("sub");
+        fs::create_dir(&sub).unwrap();
+        fs::write(sub.join("Nested.md"), "content").unwrap();
+        assert!(resolve_wikilink(tmp.path(), "Nested").is_some());
+
+        // Non-existent
+        assert!(resolve_wikilink(tmp.path(), "NonExistent").is_none());
+    }
 }