# Session Report

**Session ID:** 6ed0f2f5-e7ce-45ef-9512-ef5533648cbe

---

## Step 1: User Turn

### System Prompt

```
You are an expert Haskell and Bash programmer specialized in writing clean, idiomatic, and efficient Haskell code.
When writing Bash code:
- Avoid bash-specific logic but bash-ism are fine.
- Document required shell tools at the top of the bash script.
When writing Haskell code:
- Use modern Haskell practices (base >= 4.14)
- Prefer pure functions and explicit type signatures
- Use standard libraries when appropriate
- Add clear comments for complex logic
- Follow consistent formatting
Use list-files to explore the project structure, read-file to understand existing code, write-file to create or modify files, and check-code to verify your work.
Always compile code before considering the job done.
Your last message will serve as git-commit. Format your final message as follows:
- Start with a one-liner commit message in imperative mode (e.g., 'Fix bug in user authentication')
- The one-liner should reference the fixed issue (e.g., 'Fix bug in user authentication (#12345)')
- Follow with a blank line, then a body with a nice summary of the changes
- In the body, reference the fixed issue using 'Closes #12345' format

Example format:
Fix critical bug in session handling (#75)

This commit resolves the memory leak caused by not properly
closing session handles. The fix ensures all resources are
released when a session is terminated.

Closes #75
```

### User Query

# Implement two-phase AgentTree loading with reference validation

## Summary

Implement the two-phase loading algorithm for `AgentTree` that handles cyclic agent references through the registry, and add validation to ensure all referenced agents (both from `toolDirectory` and `extra-agents`) are properly resolved.

## Motivation

With the addition of `extra-agents` configuration and the `RuntimeRegistry`, we need to:
1. Load all agent configurations first (without full runtime initialization)
2. Resolve all references to ensure no dangling slugs
3. Initialize runtimes with tools wired via the registry

This is the core implementation that ties together the configuration changes, registry infrastructure, and context enhancements.

## Proposed Algorithm

### Phase 0: Configuration Discovery

Collect all agent configurations before creating any runtimes:

```haskell
-- | Result of the discovery phase
data AgentConfigGraph = AgentConfigGraph
    { graphNodes :: Map.Map AgentSlug AgentConfigTree
    -- ^ All agents by slug
    , graphEdges :: Map.Map AgentSlug [AgentSlug]
    -- ^ References from each agent to others (children + extra-agents)
    }

-- | Discover all agents starting from root
discoverAgentConfigs :: Props -> IO (Either (NonEmpty LoadingError) AgentConfigGraph)
discoverAgentConfigs props = do
    -- BFS/DFS traversal following both toolDirectory and extra-agents
    -- Build the graph without creating any runtimes
    undefined  -- Implementation needed
```

### Phase 1: Reference Validation

Ensure all referenced agents exist:

```haskell
-- | Validation error types
data ReferenceError
    = MissingAgentReference AgentSlug FilePath AgentSlug
    -- ^ Agent in file references missing slug
    | DuplicateAgentSlug AgentSlug [FilePath]
    -- ^ Same slug defined in multiple files
    | CyclicReference [AgentSlug]
    -- ^ Cycle detected in references (optional warning)
    deriving (Show)

-- | Validate the configuration graph
validateReferences :: AgentConfigGraph -> Either (NonEmpty LoadingError) ()
validateReferences graph = do
    -- Check all edges point to existing nodes
    -- Check for duplicate slugs
    -- Optionally detect cycles (cycles are allowed but worth warning about)
    undefined  -- Implementation needed
```

### Phase 2: Runtime Shell Creation

Create runtimes with deferred tool resolution:

```haskell
-- | Create runtime shells for all agents
createRuntimeShells :: 
    Props -> 
    AgentConfigGraph -> 
    IO (Either (NonEmpty LoadingError) (Map.Map AgentSlug Runtime))
createRuntimeShells props graph = do
    -- For each agent in graph:
    --   1. Create runtime with empty/mutable tool list
    --   2. Register in RuntimeRegistry
    --   3. Store in result map
    undefined  -- Implementation needed
```

### Phase 3: Tool Wiring

Wire up all tool references via the registry:

```haskell
-- | Wire up tool references for all runtimes
wireToolReferences ::
    Props ->
    AgentConfigGraph ->
    Map.Map AgentSlug Runtime ->
    IO ()
wireToolReferences props graph runtimes = do
    -- For each agent:
    --   1. Get its runtime from the map
    --   2. Collect all referenced agent runtimes (children + extra-agents)
    --   3. Use registry to look up each referenced runtime
    --   4. Create tool registrations via agentToTool
    --   5. Update runtime's agentTools IO action
    undefined  -- Implementation needed
```

### Phase 4: Build AgentTree

Construct the final tree structure:

```haskell
-- | Build the tree from the graph and initialized runtimes
buildAgentTree ::
    AgentConfigGraph ->
    Map.Map AgentSlug Runtime ->
    Either (NonEmpty LoadingError) AgentTree
buildAgentTree graph runtimes = do
    -- Find root agent
    -- Recursively build tree structure using graphEdges
    -- Attach runtimes from the map
    undefined  -- Implementation needed
```

## Modified Entry Point

```haskell
loadAgentTreeRuntime :: Props -> IO LoadAgentResult
loadAgentTreeRuntime props = do
    -- Create registry
    registry <- newRuntimeRegistry
    let propsWithRegistry = props{runtimeRegistry = registry}
    
    -- Phase 0: Discover all configs
    graphResult <- discoverAgentConfigs propsWithRegistry
    case graphResult of
        Left errs -> pure $ Errors errs
        Right graph -> do
            -- Phase 1: Validate references
            case validateReferences graph of
                Left errs -> pure $ Errors errs
                Right () -> do
                    runTracer props.interactiveTracer (ConfigLoadedTrace graph)
                    
                    -- Phase 2: Create runtime shells
                    shellsResult <- createRuntimeShells propsWithRegistry graph
                    case shellsResult of
                        Left errs -> pure $ Errors errs
                        Right runtimes -> do
                            -- Phase 3: Wire tool references
                            wireToolReferences propsWithRegistry graph runtimes
                            
                            -- Phase 4: Build final tree
                            case buildAgentTree graph runtimes of
                                Left errs -> pure $ Errors errs
                                Right tree -> pure $ Initialized tree
```

## Data Types Reference

Key types from other modules needed for this implementation:

```haskell
-- From System.Agents.Base
AgentSlug :: Text
newtype AgentId = AgentId UUID

data Agent = Agent
    { slug :: Text
    , toolDirectory :: FilePath
    , extraAgents :: Maybe [ExtraAgentRef]
    -- ^ References to agents outside toolDirectory
    }

data ExtraAgentRef = ExtraAgentRef
    { extraAgentSlug :: AgentSlug
    , extraAgentPath :: FilePath
    }

-- From System.Agents.AgentTree
data Props = Props
    { apiKeys :: LoadedApiKeys
    , rootAgentFile :: FilePath
    , interactiveTracer :: Tracer IO Trace
    , agentToTool :: Runtime -> AgentSlug -> AgentId -> ToolRegistration
    , runtimeRegistry :: RuntimeRegistry
    }

type RuntimeRegistry = IORef (Map.Map AgentSlug Runtime)

data AgentTree = AgentTree
    { agentFile :: FilePath
    , agentBase :: Agent
    , agentRuntime :: Runtime.Runtime
    , agentChildren :: [AgentTree]
    , agentExtraRefs :: [AgentSlug]
    }

data AgentConfigTree = AgentConfigTree
    { agentConfigFile :: FilePath
    , agentConfig :: Agent
    , agentConfigChildren :: [AgentConfigTree]
    }

-- From System.Agents.Runtime.Runtime
data Runtime = Runtime
    { agentSlug :: AgentSlug
    , agentId :: AgentId
    , agentTools :: IO [ToolRegistration]
    -- ^ Mutable for deferred wiring
    }
```

## Cycle Detection Strategy

Cycles in agent references should be **allowed** but **detected and logged**:

```haskell
-- | Detect cycles for warning purposes (doesn't prevent loading)
detectCycles :: AgentConfigGraph -> [[AgentSlug]]
detectCycles graph = 
    -- Use standard cycle detection (e.g., DFS with coloring)
    -- Return list of all cycles found
    undefined

-- Usage in loadAgentTreeRuntime:
let cycles = detectCycles graph
unless (null cycles) $
    runTracer props.interactiveTracer (CyclicReferencesWarning cycles)
```

This supports the use case of intentional mutual recursion while warning about potential infinite loops.

## Acceptance Criteria

- [ ] `AgentConfigGraph` type for representing the agent reference graph
- [ ] `discoverAgentConfigs` to collect all configurations
- [ ] `validateReferences` to check for missing/duplicate references
- [ ] `ReferenceError` type with specific error messages
- [ ] `createRuntimeShells` for phase 2 initialization
- [ ] `wireToolReferences` for phase 3 tool wiring
- [ ] `buildAgentTree` for constructing final tree
- [ ] Updated `loadAgentTreeRuntime` with full multi-phase algorithm
- [ ] Cycle detection with warnings (cycles allowed)
- [ ] Tests for: valid tree, missing reference, duplicate slug, cyclic references

## Tradeoffs

| Aspect | Option A (chosen) | Option B |
|--------|-------------------|----------|
| Cycle handling | Allow with warning | Strictly forbid |
| Discovery order | BFS from root | Load all JSONs in directory |
| Validation | Fail fast on first error | Collect all errors |

**Recommended**: Allow cycles (they're useful for mutual recursion), BFS from root (respects toolDirectory hierarchy), collect all errors (better UX).

## Related

- Part of #81 (recursive references in AgentTree)
- Integrates with: `extra-agents` config, `RuntimeRegistry`, `ToolExecutionContext` depth tracking
- Final piece that enables self-references and mutual recursion




---
Please mention issue #86 in the commit message.



### Available Tools

- **bash_grep-files** (`bash_grep-files`)
  - Description: Search for a pattern in files using 'git grep'
- **bash_check-code** (`bash_check-code`)
  - Description: Check Haskell code by compiling or testing
- **bash_write-file** (`bash_write-file`)
  - Description: Write content to a file
- **bash_list-files** (`bash_list-files`)
  - Description: List all files in the project
- **bash_read-file** (`bash_read-file`)
  - Description: Read the contents of a file

---

## Step 2: LLM Turn

### Thinking Process

<details>
<summary>Click to expand reasoning</summary>

The user wants me to implement a two-phase AgentTree loading algorithm with reference validation. Let me first explore the project structure to understand the existing code and then implement the required changes.

Let me start by listing the files in the project.
</details>

### Response



### Tool Calls

- **bash_list-files**

---

## Step 3: User Turn



---

## Step 4: LLM Turn

### Thinking Process

<details>
<summary>Click to expand reasoning</summary>

Let me explore the key files mentioned in the issue:
1. System.Agents.AgentTree - for the Props type and loading functions
2. System.Agents.Base - for Agent and ExtraAgentRef types
3. System.Agents.Runtime.Runtime - for Runtime type

Let me read these files to understand the current implementation.
</details>

### Response



### Tool Calls

- **bash_read-file**
- **bash_read-file**
- **bash_read-file**

---

## Step 5: User Turn



---

## Step 6: LLM Turn

### Thinking Process

<details>
<summary>Click to expand reasoning</summary>

Now I have a good understanding of the existing code. Let me also check the Runtime.Trace and FileLoader modules to understand the trace types and file loading.
</details>

### Response

Let me check the FileLoader and Runtime.Trace modules to understand how file loading works:

### Tool Calls

- **bash_read-file**
- **bash_read-file**

---

## Step 7: User Turn



---

## Step 8: LLM Turn

### Thinking Process

<details>
<summary>Click to expand reasoning</summary>

Now I have a good understanding of the codebase. Let me also check the existing test file to understand the testing patterns:
</details>

### Response

Let me also check the test file and the cabal file to understand the project structure:

### Tool Calls

- **bash_read-file**
- **bash_read-file**

---

## Step 9: User Turn



---

## Step 10: LLM Turn

### Thinking Process

<details>
<summary>Click to expand reasoning</summary>

Now I have a good understanding of the codebase. Let me also check the Tools.Context module since it seems to be related to the recursion tracking mentioned in the issue.
</details>

### Response

Let me check the Tools.Context module to understand the recursion tracking:

### Tool Calls

- **bash_read-file**

---

## Step 11: User Turn



---

## Step 12: LLM Turn

### Thinking Process

<details>
<summary>Click to expand reasoning</summary>

Now I have a comprehensive understanding of the codebase. Let me implement the two-phase loading algorithm as described in the issue. I need to:

1. Create `AgentConfigGraph` type for representing the agent reference graph
2. Implement `discoverAgentConfigs` to collect all configurations
3. Implement `validateReferences` to check for missing/duplicate references
4. Create `ReferenceError` type with specific error messages
5. Implement `createRuntimeShells` for phase 2 initialization
6. Implement `wireToolReferences` for phase 3 tool wiring
7. Implement `buildAgentTree` for constructing final tree
8. Update `loadAgentTreeRuntime` with full multi-phase algorithm
9. Add cycle detection with warnings
10. Add tests for the new functionality

Let me now write the implementation:
</details>

### Response

Now I have a comprehensive understanding of the codebase. Let me implement the two-phase loading algorithm with reference validation. I'll update the AgentTree module with all the required changes.

### Tool Calls

- **bash_write-file**

---

## Step 13: User Turn



---

## Step 14: LLM Turn

### Thinking Process

<details>
<summary>Click to expand reasoning</summary>

Now let me compile the code to check for any errors.
</details>

### Response

Now let me compile the code to check for any errors:

### Tool Calls

- **bash_check-code**

---

## Step 15: User Turn



---

## Step 16: LLM Turn

### Thinking Process

<details>
<summary>Click to expand reasoning</summary>

I have a type error - I need to check the Runtime.Trace type and ensure that AgentTrace is correctly mapping from Runtime.Trace to Trace. Let me check the Runtime module to understand the expected trace type.

Looking at the error, the issue is that `initAgentTreeAgentDeferred` expects a `Tracer IO Trace` but I'm passing a tracer that contramaps from `Runtime.Trace` to `Trace`. Let me check the signature.

Looking at the original code in the file, the `initAgentTreeAgentDeferred` function is using `contramap AgentTrace tracer` where `tracer` is `Tracer IO Trace` from the Props. This should work because `AgentTrace :: Runtime.Trace -> Trace`.

Wait, let me look at the issue more carefully. The problem is that `initAgentTreeAgentDeferred` takes `Tracer IO Trace` (from Props), not `Tracer IO Runtime.Trace`.

Looking at the definition:
```haskell
initAgentTreeAgentDeferred ::
    Tracer IO Trace ->  -- This expects Trace, not Runtime.Trace
```

So I need to pass the tracer directly without contramapping again since it's already `Tracer IO Trace`.

Let me fix this.
</details>

### Response

I need to fix the type error in the `createSingleRuntime` function. The tracer should be used directly since `initAgentTreeAgentDeferred` expects `Tracer IO Trace`:

### Tool Calls

- **bash_read-file**

---

## Step 17: User Turn



---

## Step 18: LLM Turn

### Thinking Process

<details>
<summary>Click to expand reasoning</summary>

I see the issue. The `initAgentTreeAgentDeferred` function takes `Tracer IO Trace` but internally it uses `contramap AgentTrace tracer` where `AgentTrace :: Runtime.Trace -> Trace`. So the tracer passed in must be `Tracer IO Trace`.

But the problem is that in `createSingleRuntime`, I'm doing:
```haskell
(contramap AgentTrace props.interactiveTracer)
```

This tries to contramap from `Trace -> Trace` (since `props.interactiveTracer :: Tracer IO Trace`), which doesn't match the expected `Runtime.Trace -> Trace`.

The fix is simple: just pass `props.interactiveTracer` directly without the contramap.

Let me update the code.
</details>

### Response

I see the issue - in `createSingleRuntime`, I'm contramapping twice. The `initAgentTreeAgentDeferred` function already does the contramapping internally. Let me fix it:

### Tool Calls

- **bash_write-file**

---

## Step 19: User Turn



---

## Step 20: LLM Turn

### Thinking Process

<details>
<summary>Click to expand reasoning</summary>

Now let me compile again to check for any remaining errors.
</details>

### Response



### Tool Calls

- **bash_check-code**

---

## Step 21: User Turn



---

## Step 22: LLM Turn

### Thinking Process

<details>
<summary>Click to expand reasoning</summary>

The code compiles now. There are some warnings about unused variables and incomplete pattern matches (which are in other modules and pre-existing), but the main functionality compiles. Let me now add tests for the new functionality as required by the acceptance criteria.
</details>

### Response

The code compiles. Now let me add tests for the new two-phase loading functionality:

### Tool Calls

- **bash_read-file**

---

## Step 23: User Turn



---

## Step 24: LLM Turn

### Thinking Process

<details>
<summary>Click to expand reasoning</summary>

Now I need to add tests for the two-phase loading algorithm. I'll add tests for:
1. Valid tree
2. Missing reference
3. Duplicate slug
4. Cyclic references

Let me create a comprehensive test file.
</details>

### Response



### Tool Calls

- **bash_write-file**

---

## Step 25: User Turn



---

## Step 26: LLM Turn

### Thinking Process

<details>
<summary>Click to expand reasoning</summary>

Now let me run the tests to make sure they pass.
</details>

### Response



### Tool Calls

- **bash_check-code**

---

## Step 27: User Turn



---

## Step 28: LLM Turn

### Thinking Process

<details>
<summary>Click to expand reasoning</summary>

I need to add `containers` to the test dependencies in the cabal file.
</details>

### Response

I need to add `containers` to the test dependencies in the cabal file:

### Tool Calls

- **bash_read-file**

---

## Step 29: User Turn



---

## Step 30: LLM Turn

### Thinking Process

<details>
<summary>Click to expand reasoning</summary>

I need to add `containers` to the test suite's build-depends.
</details>

### Response



### Tool Calls

- **bash_write-file**

---

## Step 31: User Turn



---

## Step 32: LLM Turn

### Thinking Process

<details>
<summary>Click to expand reasoning</summary>

Now let me run the tests again.
</details>

### Response



### Tool Calls

- **bash_check-code**

---

## Step 33: User Turn



---

## Step 34: LLM Turn

### Thinking Process

<details>
<summary>Click to expand reasoning</summary>

I see the issue - the `AgentConfigNode` type and its fields are not exported from the `AgentTree` module. I need to add them to the export list. Let me update the AgentTree module.
</details>

### Response

I need to export the `AgentConfigNode` type and its fields from the AgentTree module:

### Tool Calls

- **bash_read-file**

---

## Step 35: User Turn



---

## Step 36: LLM Turn

### Thinking Process

<details>
<summary>Click to expand reasoning</summary>

I see the issue - I need to export `AgentConfigNode(..)` and `ReferenceValidationTrace(..)` from the module. Let me update the export list.
</details>

### Response

I need to export `AgentConfigNode` and `ReferenceValidationTrace` with their constructors:

### Tool Calls

- **bash_write-file**

---

## Step 37: User Turn



---

## Step 38: LLM Turn

### Thinking Process

<details>
<summary>Click to expand reasoning</summary>

Now let me run the tests again to check if they pass.
</details>

### Response



### Tool Calls

- **bash_check-code**

---

## Step 39: User Turn



---

## Step 40: LLM Turn

### Thinking Process

<details>
<summary>Click to expand reasoning</summary>

All 46 tests passed! The implementation is complete. Let me now write the final git commit message summarizing the changes.
</details>

### Response

All tests pass. Let me verify the final compilation is successful:

### Tool Calls

- **bash_check-code**

---

## Step 41: User Turn



---

## Step 42: LLM Turn

### Thinking Process

<details>
<summary>Click to expand reasoning</summary>

The code compiles successfully. The warnings are in the app/Main.hs file and are pre-existing (not related to my changes). My implementation is complete.

Let me now summarize the changes I made in the final commit message.
</details>

### Response

The implementation is complete and all tests pass. Here's a summary of the changes:

Implement two-phase AgentTree loading with reference validation (#86)

This commit implements the two-phase loading algorithm for AgentTree that
handles cyclic agent references through the registry, and adds validation
to ensure all referenced agents are properly resolved.

Key changes:

1. **New Data Types**:
   - `AgentConfigGraph`: Represents the agent reference graph with nodes (agents)
     and edges (references)
   - `AgentConfigNode`: A node containing file path, config, children, and extra refs
   - `ReferenceError`: Validation errors including `MissingAgentReference` and
     `DuplicateAgentSlug`

2. **Four-Phase Loading Algorithm**:
   - **Phase 0** (`discoverAgentConfigs`): BFS traversal to collect all agent
     configurations without creating runtimes
   - **Phase 1** (`validateReferences`): Validates all references point to
     existing nodes (no missing slugs)
   - **Phase 2** (`createRuntimeShells`): Creates runtime shells for all agents
     and registers them in the RuntimeRegistry
   - **Phase 3** (`wireToolReferences`): Wires up tool references via registry
     lookup
   - **Phase 4** (`buildAgentTree`): Constructs the final tree structure

3. **Cycle Detection** (`detectCycles`): Uses DFS with three-color marking to
   detect cycles for warning purposes. Cycles are allowed but logged to support
   intentional mutual recursion.

4. **Updated Entry Point** (`loadAgentTreeRuntime`): Implements the full
   multi-phase algorithm with tracing for each phase

5. **Tests**: Added comprehensive tests for:
   - `AgentConfigGraph` construction
   - Reference validation (valid tree, missing reference, duplicate slug)
   - Cycle detection (linear chain, self-reference, mutual reference,
     complex graphs)

Closes #86
