feat: Externalize research tool as embedded skill

Replaces the built-in research/research_status tools with a portable
skill-based approach:

- Add embedded skills infrastructure (skills compiled into binary)
- Add repo-local skills/ directory support (highest priority)
- Create research skill with SKILL.md and g3-research shell script
- Script extraction to .g3/bin/ with version tracking
- Filesystem-based handoff via .g3/research/<id>/status.json
- Remove PendingResearchManager and all research tool code
- Update system prompt to reference skill instead of tool

Benefits:
- No special tool infrastructure needed (just shell + read_file)
- Context-efficient (reports stay on disk until needed)
- Crash-resilient (state persisted to filesystem)
- Portable (skill can be overridden per-workspace)

Breaking change: research tool calls now return a deprecation message
pointing to the research skill.

crates/g3-core/src/skills/embedded.rs

@@ -0,0 +1,87 @@
+//! Embedded skills - compiled into the binary for portability.
+//!
+//! Core skills are embedded at compile time using `include_str!`.
+//! This ensures g3 works anywhere without needing external skill files.
+//!
+//! Priority order (highest to lowest):
+//! 1. Repo `skills/` directory (on disk, checked into git)
+//! 2. Workspace `.g3/skills/` directory
+//! 3. Config extra_paths
+//! 4. Global `~/.g3/skills/` directory
+//! 5. Embedded skills (this module - always available)
+
+use std::collections::HashMap;
+
+/// An embedded skill with its SKILL.md content and optional scripts.
+#[derive(Debug, Clone)]
+pub struct EmbeddedSkill {
+    /// Skill name (must match the name in SKILL.md frontmatter)
+    pub name: &'static str,
+    /// Content of SKILL.md
+    pub skill_md: &'static str,
+    /// Scripts bundled with the skill: (filename, content)
+    pub scripts: &'static [(&'static str, &'static str)],
+}
+
+/// All embedded skills, compiled into the binary.
+///
+/// To add a new embedded skill:
+/// 1. Create `skills/<name>/SKILL.md` in the repo
+/// 2. Add an entry here with `include_str!`
+static EMBEDDED_SKILLS: &[EmbeddedSkill] = &[
+    EmbeddedSkill {
+        name: "research",
+        skill_md: include_str!("../../../../skills/research/SKILL.md"),
+        scripts: &[
+            ("g3-research", include_str!("../../../../skills/research/g3-research")),
+        ],
+    },
+];
+
+/// Get all embedded skills.
+pub fn get_embedded_skills() -> &'static [EmbeddedSkill] {
+    EMBEDDED_SKILLS
+}
+
+/// Get an embedded skill by name.
+pub fn get_embedded_skill(name: &str) -> Option<&'static EmbeddedSkill> {
+    EMBEDDED_SKILLS.iter().find(|s| s.name == name)
+}
+
+/// Get embedded skills as a map for easy lookup.
+pub fn get_embedded_skills_map() -> HashMap<&'static str, &'static EmbeddedSkill> {
+    EMBEDDED_SKILLS.iter().map(|s| (s.name, s)).collect()
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn test_embedded_skills_exist() {
+        let skills = get_embedded_skills();
+        assert!(!skills.is_empty(), "Should have at least one embedded skill");
+    }
+
+    #[test]
+    fn test_research_skill_embedded() {
+        let skill = get_embedded_skill("research");
+        assert!(skill.is_some(), "Research skill should be embedded");
+        
+        let skill = skill.unwrap();
+        assert!(skill.skill_md.contains("name: research"), "SKILL.md should have name field");
+        assert!(!skill.scripts.is_empty(), "Research skill should have scripts");
+    }
+
+    #[test]
+    fn test_get_by_name() {
+        assert!(get_embedded_skill("research").is_some());
+        assert!(get_embedded_skill("nonexistent").is_none());
+    }
+
+    #[test]
+    fn test_skills_map() {
+        let map = get_embedded_skills_map();
+        assert!(map.contains_key("research"));
+    }
+}