refactor(git): expand hook sync with skill scanning and multi-root discovery

Update sync module to support .claude/skills and .codex/skills roots,
add system/source tracking to discovered skills, and refactor
migration path for the new SQL-file based migrator.

libs/git/hook/sync/mod.rs

@@ -23,12 +23,16 @@ use crate::GitDomain;
 
 use sha1::Digest;
 
+const SKILL_ROOTS: &[(&str, &str)] = &[(".claude/skills", "claude"), (".codex/skills", "codex")];
+const ROOT_SKILL_SYSTEM: &str = "root";
+
 fn should_descend_dir(name: &str) -> bool {
     name != ".git"
 }
 
-/// Recursively scan `base` for files named `SKILL.md`.
-/// The skill slug is `{short_repo_id}/{parent_dir_name}` to ensure uniqueness across repos.
+/// Recursively scan supported skill locations for files named `SKILL.md`.
+/// Root-level skill packs keep the legacy slug `{short_repo_id}/{skill_dir}`.
+/// System skills use `{short_repo_id}/{system}/{relative_skill_dir}`.
 fn scan_skills_from_dir(
     base: &Path,
     repo_id: &RepoId,
@@ -36,8 +40,34 @@ fn scan_skills_from_dir(
 ) -> Result<Vec<DiscoveredSkill>, std::io::Error> {
     let repo_id_prefix = &repo_id.to_string()[..8];
     let mut discovered = Vec::new();
-    let mut stack = vec![base.to_path_buf()];
 
+    for (root, system) in SKILL_ROOTS {
+        let root_path = base.join(root);
+        if root_path.exists() {
+            scan_skill_root_from_dir(
+                &root_path,
+                repo_id_prefix,
+                system,
+                root,
+                commit_sha,
+                &mut discovered,
+            );
+        }
+    }
+    scan_root_skill_pack_from_dir(base, repo_id_prefix, commit_sha, &mut discovered);
+
+    Ok(discovered)
+}
+
+fn scan_skill_root_from_dir(
+    root_path: &Path,
+    repo_id_prefix: &str,
+    system: &str,
+    root: &str,
+    commit_sha: &str,
+    discovered: &mut Vec<DiscoveredSkill>,
+) {
+    let mut stack = vec![root_path.to_path_buf()];
     while let Some(dir) = stack.pop() {
         let entries = match std::fs::read_dir(&dir) {
             Ok(e) => e,
@@ -47,30 +77,82 @@ fn scan_skills_from_dir(
             let path = entry.path();
             if path.is_dir() {
                 stack.push(path);
-            } else if path
-                .file_name()
-                .and_then(|n| n.to_str())
-                .map(|x| x.to_lowercase())
-                == Some("skill.md".to_string())
-            {
-                if let Some(dir_name) = path
-                    .parent()
-                    .and_then(|p| p.file_name())
-                    .and_then(|n| n.to_str())
-                {
-                    let slug = format!("{}/{}", repo_id_prefix, dir_name);
+                continue;
+            }
+            if !is_skill_file_name(&path) {
+                continue;
+            }
+            let Some(parent) = path.parent() else {
+                continue;
+            };
+            let relative_skill_dir = parent
+                .strip_prefix(root_path)
+                .ok()
+                .and_then(path_to_slug)
+                .filter(|s| !s.is_empty());
+            let Some(relative_skill_dir) = relative_skill_dir else {
+                continue;
+            };
+            let slug = format!("{}/{}/{}", repo_id_prefix, system, relative_skill_dir);
             if let Ok(raw) = std::fs::read(&path) {
                 let blob_hash = git_blob_hash(&raw);
                 let mut skill = parse_skill_content(&slug, &raw);
                 skill.commit_sha = Some(commit_sha.to_string());
                 skill.blob_hash = Some(blob_hash);
+                skill.metadata = enrich_metadata(
+                    skill.metadata,
+                    system,
+                    Some(&format!("{}/{}/SKILL.md", root, relative_skill_dir)),
+                );
                 discovered.push(skill);
             }
         }
     }
+}
+
+fn scan_root_skill_pack_from_dir(
+    base: &Path,
+    repo_id_prefix: &str,
+    commit_sha: &str,
+    discovered: &mut Vec<DiscoveredSkill>,
+) {
+    let entries = match std::fs::read_dir(base) {
+        Ok(e) => e,
+        Err(_) => return,
+    };
+    for entry in entries.flatten() {
+        let path = entry.path();
+        if !path.is_dir() {
+            continue;
+        }
+        let Some(dir_name) = path.file_name().and_then(|n| n.to_str()) else {
+            continue;
+        };
+        if dir_name == ".git" || dir_name == ".claude" || dir_name == ".codex" {
+            continue;
+        }
+        let skill_file = path.join("SKILL.md");
+        if !skill_file.exists() {
+            continue;
+        }
+        let relative_skill_dir = slugify_segment(dir_name);
+        if relative_skill_dir.is_empty() {
+            continue;
+        }
+        let slug = format!("{}/{}", repo_id_prefix, relative_skill_dir);
+        if let Ok(raw) = std::fs::read(&skill_file) {
+            let blob_hash = git_blob_hash(&raw);
+            let mut skill = parse_skill_content(&slug, &raw);
+            skill.commit_sha = Some(commit_sha.to_string());
+            skill.blob_hash = Some(blob_hash);
+            skill.metadata = enrich_metadata(
+                skill.metadata,
+                ROOT_SKILL_SYSTEM,
+                Some(&format!("{}/SKILL.md", relative_skill_dir)),
+            );
+            discovered.push(skill);
         }
     }
-    Ok(discovered)
 }
 
 fn git_blob_hash(content: &[u8]) -> String {
@@ -126,6 +208,57 @@ struct DiscoveredSkill {
     blob_hash: Option<String>,
 }
 
+fn is_skill_file_name(path: &Path) -> bool {
+    path.file_name()
+        .and_then(|n| n.to_str())
+        .is_some_and(|name| name.eq_ignore_ascii_case("SKILL.md"))
+}
+
+fn path_to_slug(path: &Path) -> Option<String> {
+    let parts: Vec<String> = path
+        .components()
+        .filter_map(|c| c.as_os_str().to_str())
+        .map(slugify_segment)
+        .filter(|s| !s.is_empty())
+        .collect();
+    (!parts.is_empty()).then(|| parts.join("/"))
+}
+
+fn slugify_segment(input: &str) -> String {
+    let mut out = String::with_capacity(input.len());
+    let mut last_dash = false;
+    for ch in input.chars() {
+        let ch = ch.to_ascii_lowercase();
+        if ch.is_ascii_alphanumeric() || ch == '_' || ch == '-' {
+            out.push(ch);
+            last_dash = false;
+        } else if !last_dash {
+            out.push('-');
+            last_dash = true;
+        }
+    }
+    out.trim_matches('-').to_string()
+}
+
+fn enrich_metadata(
+    mut metadata: serde_json::Value,
+    system: &str,
+    relative_path: Option<&str>,
+) -> serde_json::Value {
+    if !metadata.is_object() {
+        metadata = serde_json::json!({});
+    }
+    if let Some(obj) = metadata.as_object_mut() {
+        obj.entry("system")
+            .or_insert_with(|| serde_json::Value::String(system.to_string()));
+        if let Some(relative_path) = relative_path {
+            obj.entry("path")
+                .or_insert_with(|| serde_json::Value::String(relative_path.to_string()));
+        }
+    }
+    metadata
+}
+
 fn extract_frontmatter(raw: &str) -> (Option<&str>, &str) {
     let trimmed = raw.trim_start();
     if !trimmed.starts_with("---") {
@@ -175,20 +308,25 @@ fn scan_skills_from_tree(
                         }
                     }
                 }
-                Some(git2::ObjectType::Blob) if name.to_lowercase() == "skill.md" => {
-                    let dir_name = std::path::Path::new(&entry_path)
-                        .parent()
-                        .and_then(|p| p.file_name())
-                        .and_then(|n| n.to_str());
-                    let Some(dir_name) = dir_name else { continue };
+                Some(git2::ObjectType::Blob) if name.eq_ignore_ascii_case("SKILL.md") => {
+                    let Some((system, relative_skill_dir, legacy_slug)) =
+                        skill_location_from_path(&entry_path)
+                    else {
+                        continue;
+                    };
 
-                    let slug = format!("{}/{}", repo_id_prefix, dir_name);
+                    let slug = if legacy_slug {
+                        format!("{}/{}", repo_id_prefix, relative_skill_dir)
+                    } else {
+                        format!("{}/{}/{}", repo_id_prefix, system, relative_skill_dir)
+                    };
                     if let Ok(blob) = entry.to_object(git_repo).and_then(|o| o.peel_to_blob()) {
                         let raw = blob.content();
                         let blob_hash = git_blob_hash(raw);
                         let mut skill = parse_skill_content(&slug, raw);
                         skill.commit_sha = Some(commit_sha.to_string());
                         skill.blob_hash = Some(blob_hash);
+                        skill.metadata = enrich_metadata(skill.metadata, system, Some(&entry_path));
                         discovered.push(skill);
                     }
                 }
@@ -200,6 +338,39 @@ fn scan_skills_from_tree(
     Ok(discovered)
 }
 
+fn skill_location_from_path(path: &str) -> Option<(&'static str, String, bool)> {
+    let normalized = path.replace('\\', "/");
+    for (root, system) in SKILL_ROOTS {
+        let prefix = format!("{}/", root);
+        let suffix = "/SKILL.md";
+        if normalized.starts_with(&prefix) && normalized.ends_with(suffix) {
+            let relative = &normalized[prefix.len()..normalized.len() - suffix.len()];
+            let slug = relative
+                .split('/')
+                .map(slugify_segment)
+                .filter(|s| !s.is_empty())
+                .collect::<Vec<_>>()
+                .join("/");
+            if !slug.is_empty() {
+                return Some((*system, slug, false));
+            }
+        }
+    }
+
+    let suffix = "/SKILL.md";
+    if normalized.ends_with(suffix) && !normalized.starts_with('.') {
+        let relative = &normalized[..normalized.len() - suffix.len()];
+        if !relative.contains('/') {
+            let slug = slugify_segment(relative);
+            if !slug.is_empty() {
+                return Some((ROOT_SKILL_SYSTEM, slug, true));
+            }
+        }
+    }
+
+    None
+}
+
 #[derive(Clone)]
 pub struct HookMetaDataSync {
     pub db: AppDatabase,
@@ -414,40 +585,27 @@ impl HookMetaDataSync {
             }
         };
 
-        // Deduplicate by {repo_id}+{blob_hash}, keep latest by commit_sha
+        // Deduplicate by stable slug. Blob hash changes when content changes and must not be the
+        // upsert key because project_skill has a unique (project_uuid, slug) constraint.
         let mut deduped: std::collections::HashMap<String, DiscoveredSkill> =
             std::collections::HashMap::new();
         for skill in discovered {
-            let key = if let Some(ref hash) = skill.blob_hash {
-                format!("{}:{}", self.repo.id, hash)
-            } else {
-                format!("{}:{}:slug", self.repo.id, skill.slug)
-            };
-            match deduped.get(&key) {
+            match deduped.get(&skill.slug) {
                 Some(existing) => {
                     if skill.commit_sha.as_ref().unwrap_or(&String::new())
                         > existing.commit_sha.as_ref().unwrap_or(&String::new())
                     {
-                        deduped.insert(key, skill);
+                        deduped.insert(skill.slug.clone(), skill);
                     }
                 }
                 None => {
-                    deduped.insert(key, skill);
+                    deduped.insert(skill.slug.clone(), skill);
                 }
             }
         }
 
-        let existing_by_hash: HashMap<_, _> = existing
-            .into_iter()
-            .map(|s| {
-                let key = format!(
-                    "{}:{}",
-                    s.repo_id.unwrap_or_default(),
-                    s.blob_hash.clone().unwrap_or_default()
-                );
-                (key, s)
-            })
-            .collect();
+        let existing_by_slug: HashMap<_, _> =
+            existing.into_iter().map(|s| (s.slug.clone(), s)).collect();
 
         let mut seen_keys = std::collections::HashSet::new();
 
@@ -455,12 +613,17 @@ impl HookMetaDataSync {
             seen_keys.insert(key.clone());
             let json_meta = serde_json::to_value(&skill.metadata).unwrap_or_default();
 
-            if let Some(existing_skill) = existing_by_hash.get(&key) {
+            if let Some(existing_skill) = existing_by_slug.get(&key) {
                 if existing_skill.content != skill.content
                     || existing_skill.metadata != json_meta
                     || existing_skill.commit_sha != skill.commit_sha
+                    || existing_skill.blob_hash != skill.blob_hash
+                    || existing_skill.name != skill.name
+                    || existing_skill.description != skill.description
                 {
                     let mut active: SkillActiveModel = existing_skill.clone().into();
+                    active.name = Set(skill.name);
+                    active.description = Set(skill.description);
                     active.content = Set(skill.content);
                     active.metadata = Set(json_meta);
                     active.commit_sha = Set(skill.commit_sha);
@@ -494,7 +657,7 @@ impl HookMetaDataSync {
             }
         }
 
-        for (key, old_skill) in existing_by_hash {
+        for (key, old_skill) in existing_by_slug {
             if !seen_keys.contains(&key) {
                 if SkillEntity::delete_by_id(old_skill.id)
                     .exec(&self.db)