Fix stale docs

CHANGELOG.md

@@ -3,9 +3,10 @@
 
 ### Added
 
-- **RAG skill** (`haiku.rag.skills.rag`): haiku.skills integration with search, list_documents, get_document, ask, analyze, and research tools plus managed `RAGState`
+- **RAG skill** (`haiku.rag.skills.rag`): haiku.skills integration with search, list_documents, get_document, ask, and research tools plus managed `RAGState`
+- **RLM skill** (`haiku.rag.skills.rlm`): haiku.skills integration with analyze tool for computational analysis via code execution
 - **`HaikuRAG.research()`**: Client method for multi-agent research
-- **haiku.skills entry point**: `rag = "haiku.rag.skills.rag:create_skill"`
+- **haiku.skills entry points**: `rag = "haiku.rag.skills.rag:create_skill"`, `rag-rlm = "haiku.rag.skills.rlm:create_skill"`
 
 ### Changed
 

README.md

@@ -137,7 +137,7 @@ Full documentation at: https://ggozad.github.io/haiku.rag/
 - [Configuration](https://ggozad.github.io/haiku.rag/configuration/) - YAML configuration
 - [CLI](https://ggozad.github.io/haiku.rag/cli/) - Command reference
 - [Python API](https://ggozad.github.io/haiku.rag/python/) - Complete API docs
-- [Agents](https://ggozad.github.io/haiku.rag/agents/) - QA, chat, and research agents
+- [Agents](https://ggozad.github.io/haiku.rag/agents/) - QA and research agents
 - [RLM Agent](https://ggozad.github.io/haiku.rag/rlm/) - Complex analytical tasks via code execution
 - [Applications](https://ggozad.github.io/haiku.rag/apps/) - Chat TUI, web app, and inspector
 - [Server](https://ggozad.github.io/haiku.rag/server/) - File monitoring and MCP

app/README.md

@@ -46,7 +46,7 @@ A conversational RAG interface built with [CopilotKit](https://copilotkit.ai/) a
 
 ### haiku.rag.yaml
 
-Configure the chat agent's LLM, embeddings, and search settings:
+Configure the LLM, embeddings, and search settings:
 
 ```yaml
 qa:
@@ -100,7 +100,7 @@ docker compose -f docker-compose.dev.yml up -d --build
 
 ## Chat Capabilities
 
-The chat agent can:
+The chat can:
 
 - **Search** your documents with hybrid vector + full-text search
 - **Answer questions** with citations from your knowledge base

docs/cli.md

@@ -164,11 +164,6 @@ haiku-rag chat
 haiku-rag chat --db /path/to/database.lancedb
 ```
 
-Provide initial background context for the conversation:
-```bash
-haiku-rag chat --initial-context "Focus on Python programming concepts"
-```
-
 !!! note
     Requires the `tui` extra: `pip install haiku.rag-slim[tui]` (included in full `haiku.rag` package)
 
@@ -178,18 +173,6 @@ The chat interface provides:
 - Expandable citations with source metadata
 - Session memory for context-aware follow-up questions
 - Visual grounding to inspect chunk source locations
-- Initial context that can be edited before the first message
-
-**Initial Context Behavior:**
-
-- Edit initial context via command palette before sending your first message
-- Once you send a message, initial context becomes read-only
-- The agent uses initial context as a starting point for session summarization
-- Clearing chat resets to the CLI-provided context and unlocks editing
-
-Flags:
-
-- `--initial-context`: Initial background context for the conversation (editable until first message)
 
 See [Applications](apps.md#chat-tui) for keyboard shortcuts and features.
 

docs/python.md

@@ -448,4 +448,4 @@ agent = Agent(
 result = await agent.run("What are the main findings?")
 ```
 
-See [Tools & Skills](tools.md) for the full API reference.
+See [Toolsets](tools.md) for the full API reference.

haiku_rag_slim/haiku/rag/agents/research/models.py

@@ -21,7 +21,7 @@ class IterativePlanResult(BaseModel):
 class Citation(BaseModel):
     """Resolved citation with full metadata for display/visual grounding.
 
-    Used by both research graph and chat agent. The optional index field
+    Used by research graph and chat applications. The optional index field
     supports UI display ordering in chat contexts.
     """
 

haiku_rag_slim/haiku/rag/app.py

@@ -476,8 +476,6 @@ class HaikuRAGApp:  # pragma: no cover
                     self.console.print(f"• {finding}")
                 self.console.print()
 
-            # (Themes section removed)
-
             # Conclusions
             if report.conclusions:
                 self.console.print("[bold cyan]Conclusions:[/bold cyan]")

haiku_rag_slim/haiku/rag/chat/__init__.py

@@ -14,7 +14,7 @@ def run_chat(
         db_path: Path to the LanceDB database. If None, uses default from config.
         read_only: Whether to open the database in read-only mode.
         before: Query database as it existed before this datetime.
-        model: Model to use for the chat agent.
+        model: Model to use for the chat.
     """
     try:
         from haiku.rag.chat.app import ChatApp

haiku_rag_slim/haiku/rag/cli.py

@@ -623,7 +623,7 @@ def chat(  # pragma: no cover
     model: str | None = typer.Option(
         None,
         "--model",
-        help="Model to use for the chat agent (e.g. openai:gpt-4o)",
+        help="Model to use for the chat (e.g. openai:gpt-4o)",
     ),
 ):
     """Launch the chat TUI for conversational RAG."""

tests/agents/research/test_models.py

@@ -25,7 +25,7 @@ class TestCitation:
         assert citation.index is None
 
     def test_citation_with_index(self):
-        """Test Citation can be created with index (chat agent use case)."""
+        """Test Citation can be created with index (chat use case)."""
         citation = Citation(
             index=1,
             document_id="doc-1",