Restore research as first-class tool, remove research skill

Restores the research tool that was previously externalized as a skill:

- Add pending_research.rs: PendingResearchManager with thread-safe task tracking
- Add tools/research.rs: execute_research (async), execute_research_status
- Add research/research_status tool definitions with exclude_research config
- Integrate PendingResearchManager into Agent and ToolContext
- Inject completed research results in streaming loop

Remove research skill:
- Clear EMBEDDED_SKILLS array in embedded.rs
- Delete skills/research/ directory
- Update all tests expecting embedded research skill
- Update docs and memory to reflect the change

The research tool now:
- Spawns scout agent in background tokio task
- Returns immediately with research_id
- Automatically injects results into conversation when ready
- Supports status checks via research_status tool

analysis/breaker/2025-02-05.md

@@ -1,8 +1,12 @@
 # Breaker Report: 2025-02-05
 
+> **Note**: Issue 1 below is now obsolete. The research skill was removed and replaced
+> with a first-class `research` tool in `crates/g3-core/src/tools/research.rs`.
+> The g3-research script no longer exists.
+
 Focused on changes in commits b6d2582..9443f933 (past 10 commits).
 
-## Issue 1: JSON Escaping Bug in g3-research Script
+## Issue 1: JSON Escaping Bug in g3-research Script (OBSOLETE)
 
 ### Title
 `g3-research` produces invalid JSON when query contains actual newlines
@@ -47,19 +51,19 @@ Embedded skills have non-existent file paths that agents are instructed to `read
 
 ### Repro
 ```
-# When no repo skills/ directory exists, the research skill is loaded from embedded
+# When no repo skills/ directory exists, embedded skills are loaded
 # The generated prompt contains:
 <skill>
-  <name>research</name>
+  <name>example-skill</name>
   <description>...</description>
-  <location><embedded:research>/SKILL.md</location>
+  <location><embedded:example-skill>/SKILL.md</location>
 </skill>
 
 # The prompt instructs:
 "read the full skill file using `read_file` to get detailed instructions"
 
 # Agent attempts:
-read_file("<embedded:research>/SKILL.md")
+read_file("<embedded:example-skill>/SKILL.md")
 # Result: File not found error
 ```
 

analysis/memory.md

@@ -221,9 +221,9 @@ Portable skill packages with SKILL.md + optional scripts per Agent Skills spec (
   - `discover_skills()` [38..85] - scans 5 locations: embedded → global → extra → workspace → repo
   - `load_embedded_skills()` [88..102] - synthetic path `<embedded:name>/SKILL.md`
   - `is_embedded_skill()` [161..163] - checks `<embedded:` prefix
-- `crates/g3-core/src/skills/embedded.rs` [0..87]
-  - `EmbeddedSkill` [22..28] - name, skill_md, scripts[]
-  - `EMBEDDED_SKILLS` [32..42] - static array with include_str! for research skill
+- `crates/g3-core/src/skills/embedded.rs` [0..55]
+  - `EmbeddedSkill` [15..20] - name, skill_md
+  - `EMBEDDED_SKILLS` [27] - static array (currently empty)
 - `crates/g3-core/src/skills/extraction.rs` [0..234]
   - `extract_script()` [28..85] - extracts to `.g3/bin/`, tracks version hash
   - `needs_update()` [107..118] - compares stored hash vs content
@@ -250,22 +250,25 @@ compatibility: Requires X # Optional
 # Instructions...
 ```
 
-### Research Skill (Embedded)
-Async web research via background scout agent. Externalized from core to embedded skill.
+### Research Tool (First-Class)
+Async web research via background scout agent. Implemented as a first-class tool (not a skill).
 
-- `skills/research/SKILL.md` - skill definition
-- `skills/research/g3-research` - bash script for async research
-  - `write_status()` - writes status.json
-  - `extract_report()` - extracts between markers or filters output
+- `crates/g3-core/src/pending_research.rs` [0..547]
+  - `PendingResearchManager` - thread-safe task tracking with Arc<RwLock>
+  - `ResearchTask`, `ResearchStatus` - task state (Pending/Complete/Failed)
+  - `register()`, `complete()`, `fail()`, `get()`, `list_pending()`, `take_completed()`
+  - `with_notifications()` - broadcast channel for interactive mode
+- `crates/g3-core/src/tools/research.rs` [0..471]
+  - `execute_research()` - spawns scout agent in background tokio task
+  - `execute_research_status()` - check status of pending/completed research
+  - `CONTEXT_ERROR_PATTERNS` - detects context window exhaustion
+  - `strip_ansi_codes()`, `extract_report()` - report extraction utilities
+- `crates/g3-core/src/lib.rs`
+  - `Agent.pending_research_manager` - field on Agent struct
+  - `inject_completed_research()` [781..836] - injects results as user messages
+  - `enable_research_notifications()` - for interactive mode
 
-**Usage**:
-```bash
-background_process("research-topic", ".g3/bin/g3-research 'query'")
-shell(".g3/bin/g3-research --status <id>")  # or --list
-read_file(".g3/research/<id>/report.md")
-```
-
-**Output**: `.g3/research/<id>/status.json` + `report.md`
+**Tools**: `research` (async, returns research_id), `research_status` (check pending tasks)
 
 ### Plan Mode
 Structured task planning with cognitive forcing - requires happy/negative/boundary checks.