Merge pull request #16 from link-assistant/issue-15-47049ece53b4

Add Gemini CLI to supported tools and fix Agent JSON Input status

Author: konard

README.md

@@ -1,6 +1,6 @@
 # agent-commander
 
-A JavaScript library to control agents enclosed in CLI commands like Anthropic Claude Code CLI, OpenAI Codex, OpenCode, Qwen Code, and @link-assistant/agent.
+A JavaScript library to control agents enclosed in CLI commands like Anthropic Claude Code CLI, OpenAI Codex, OpenCode, Qwen Code, Gemini CLI, and @link-assistant/agent.
 
 Built on the success of [hive-mind](https://github.com/link-assistant/hive-mind), `agent-commander` provides a flexible JavaScript interface and CLI tools for managing agent processes with various isolation levels.
 
@@ -12,6 +12,7 @@ Built on the success of [hive-mind](https://github.com/link-assistant/hive-mind)
   - `codex` - OpenAI Codex CLI
   - `opencode` - OpenCode CLI
   - `qwen` - Qwen Code CLI (Alibaba's AI coding agent)
+  - `gemini` - Gemini CLI (Google's AI coding agent)
   - `agent` - @link-assistant/agent (unrestricted OpenCode fork)
 - **Multiple Isolation Modes**:
   - No isolation (direct execution)
@@ -58,7 +59,8 @@ bun add agent-commander
 | `codex` | OpenAI Codex CLI | ✅ | ❌ | `gpt5`, `o3`, `gpt4o` |
 | `opencode` | OpenCode CLI | ✅ | ❌ | `grok`, `gemini`, `sonnet` |
 | `qwen` | Qwen Code CLI | ✅ (stream-json) | ✅ (stream-json) | `qwen3-coder`, `coder`, `gpt-4o` |
-| `agent` | @link-assistant/agent | ✅ | ❌ | `grok`, `sonnet`, `haiku` |
+| `gemini` | Gemini CLI | ✅ (stream-json) | ❌ | `flash`, `pro`, `lite` |
+| `agent` | @link-assistant/agent | ✅ | ✅ | `grok`, `sonnet`, `haiku` |
 
 ### Claude-specific Features
 
@@ -83,6 +85,28 @@ The [Qwen Code CLI](https://github.com/QwenLM/qwen-code) supports additional fea
 - **Partial messages**: Use `--include-partial-messages` with stream-json for real-time UI updates
 - **Model flexibility**: Supports Qwen3-Coder models plus OpenAI-compatible models via API
 
+### Gemini-specific Features
+
+The [Gemini CLI](https://github.com/google-gemini/gemini-cli) supports additional features:
+
+- **Stream JSON format**: Uses `--output-format stream-json` for real-time NDJSON streaming
+- **Auto-approval mode**: Use `--yolo` flag for automatic action approval (enabled by default)
+- **Sandbox mode**: Use `--sandbox` flag for secure tool execution in isolated environment
+- **Checkpointing**: Use `--checkpointing` to save project snapshots before file modifications
+- **Debug output**: Use `-d` flag for detailed debug output
+- **Model selection**: Use `-m` flag to select model (e.g., `gemini-2.5-flash`, `gemini-2.5-pro`)
+- **Interactive mode**: Use `-i` flag with prompt to start interactive session
+
+### Agent-specific Features
+
+The [@link-assistant/agent](https://github.com/link-assistant/agent) supports additional features:
+
+- **JSON Input/Output**: Accepts JSON via stdin, outputs JSON event streams (OpenCode-compatible)
+- **Unrestricted access**: No sandbox, no permissions system - full autonomous execution
+- **13 built-in tools**: Including websearch, codesearch, batch - all enabled by default
+- **MCP support**: Model Context Protocol for extending functionality with MCP servers
+- **OpenCode compatibility**: 100% compatible with OpenCode's JSON event streaming format
+
 ## CLI Usage
 
 ### start-agent
@@ -95,7 +119,7 @@ start-agent --tool claude --working-directory "/tmp/dir" --prompt "Solve the iss
 
 #### Options
 
-- `--tool <name>` - CLI tool to use (e.g., 'claude', 'codex', 'opencode', 'qwen', 'agent') [required]
+- `--tool <name>` - CLI tool to use (e.g., 'claude', 'codex', 'opencode', 'qwen', 'gemini', 'agent') [required]
 - `--working-directory <path>` - Working directory for the agent [required]
 - `--prompt <text>` - Prompt for the agent
 - `--system-prompt <text>` - System prompt for the agent
@@ -136,6 +160,11 @@ start-agent --tool agent --working-directory "/tmp/dir" --prompt "Analyze code"
 start-agent --tool qwen --working-directory "/tmp/dir" --prompt "Review this code" --model qwen3-coder
 ```
 
+**Using Gemini**
+```bash
+start-agent --tool gemini --working-directory "/tmp/dir" --prompt "Explain this code" --model flash
+```
+
 **With model fallback (Claude)**
 ```bash
 start-agent --tool claude --working-directory "/tmp/dir" \
@@ -259,6 +288,14 @@ const qwenAgent = agent({
   prompt: 'Review this code',
   model: 'qwen3-coder',
 });
+
+// Using Gemini CLI
+const geminiAgent = agent({
+  tool: 'gemini',
+  workingDirectory: '/tmp/project',
+  prompt: 'Explain this code',
+  model: 'flash',
+});
 ```
 
 ### Streaming JSON Messages
@@ -373,7 +410,7 @@ await myAgent.start({ dryRun: true });
 import { getTool, listTools, isToolSupported } from 'agent-commander';
 
 // List all available tools
-console.log(listTools()); // ['claude', 'codex', 'opencode', 'agent', 'qwen']
+console.log(listTools()); // ['claude', 'codex', 'opencode', 'agent', 'gemini', 'qwen']
 
 // Check if a tool is supported
 console.log(isToolSupported({ toolName: 'claude' })); // true
@@ -394,7 +431,7 @@ console.log(fullId); // 'claude-opus-4-5-20251101'
 Creates an agent controller.
 
 **Parameters:**
-- `options.tool` (string, required) - CLI tool to use ('claude', 'codex', 'opencode', 'qwen', 'agent')
+- `options.tool` (string, required) - CLI tool to use ('claude', 'codex', 'opencode', 'qwen', 'gemini', 'agent')
 - `options.workingDirectory` (string, required) - Working directory
 - `options.prompt` (string, optional) - Prompt for the agent
 - `options.systemPrompt` (string, optional) - System prompt
@@ -562,6 +599,7 @@ agent-commander/
 │   │   ├── codex.mjs          # Codex CLI config
 │   │   ├── opencode.mjs       # OpenCode CLI config
 │   │   ├── qwen.mjs           # Qwen Code CLI config
+│   │   ├── gemini.mjs         # Gemini CLI config
 │   │   └── agent.mjs          # @link-assistant/agent config
 │   ├── streaming/             # JSON streaming utilities
 │   │   ├── index.mjs          # Stream exports

docs/case-studies/issue-15/README.md

@@ -0,0 +1,121 @@
+# Case Study: JSON Output/Input Documentation Accuracy
+
+**Issue:** [#15 - Double check for JSON Output and JSON Input for all our tools](https://github.com/link-assistant/agent-commander/issues/15)
+
+This document captures the investigation and resolution of documentation discrepancies in the agent-commander README.md regarding JSON input/output support for supported CLI tools.
+
+## Overview
+
+The issue identified two documentation problems:
+1. **Missing Gemini CLI** - Not listed in the Supported Tools table despite being fully implemented
+2. **Incorrect Agent CLI JSON Input status** - Marked as ❌ but actually supports JSON input
+
+## Investigation Methodology
+
+### Data Collection
+
+1. **Repository Analysis**: Examined the codebase for actual tool configurations
+2. **External Verification**: Checked upstream repositories (@link-assistant/agent, google-gemini/gemini-cli)
+3. **Code Review**: Analyzed `js/src/tools/*.mjs` configuration files
+4. **Documentation Review**: Cross-referenced README.md claims with actual capabilities
+
+### Evidence Sources
+
+| Source | Location | Key Finding |
+|--------|----------|-------------|
+| agent.mjs | js/src/tools/agent.mjs:246 | `supportsJsonInput: true` |
+| gemini.mjs | js/src/tools/gemini.mjs | Full Gemini CLI implementation |
+| tools/index.mjs | js/src/tools/index.mjs:21 | Exports `geminiTool` |
+| @link-assistant/agent | GitHub README | "JSON Input/Output: Accepts JSON via stdin" |
+| google-gemini/gemini-cli | GitHub README | Supports `--output-format stream-json` |
+
+## Root Cause Analysis
+
+### Problem 1: Missing Gemini in README
+
+**Root Cause**: The Gemini CLI tool was added to the codebase in a previous update (gemini.mjs created, index.mjs updated), but the README.md Supported Tools table was not updated to include this new tool.
+
+**Evidence**:
+- `js/src/tools/gemini.mjs` exists with full implementation (318 lines)
+- `js/src/tools/index.mjs` imports and exports `geminiTool`
+- README.md table only lists: claude, codex, opencode, qwen, agent
+
+### Problem 2: Incorrect Agent JSON Input Status
+
+**Root Cause**: Documentation lag - the Agent CLI's JSON input capability was either overlooked during initial documentation or the capability was added after documentation was written.
+
+**Evidence**:
+- `js/src/tools/agent.mjs:246` explicitly states `supportsJsonInput: true`
+- @link-assistant/agent README states: "JSON Input/Output: Accepts JSON via stdin, outputs JSON event streams (OpenCode-compatible)"
+- The code comments in agent.mjs line 71 confirm: "Agent uses stdin for prompt input (NDJSON streaming supported)"
+
+## Timeline of Events
+
+1. **Initial Release**: agent-commander released with support for claude, codex, opencode, agent, qwen
+2. **Agent JSON Support**: Agent CLI implemented full JSON input/output (based on OpenCode compatibility)
+3. **Gemini Addition**: Gemini CLI tool added to codebase (gemini.mjs created)
+4. **Documentation Gap**: README.md not updated to reflect Gemini addition or Agent JSON input capability
+5. **Issue #15**: Documentation inconsistency discovered and reported
+
+## Solution Implementation
+
+### Changes Made to README.md
+
+1. **Added Gemini to Supported Tools Table**:
+   ```markdown
+   | `gemini` | Gemini CLI | ✅ (stream-json) | ❌ | `flash`, `pro`, `lite` |
+   ```
+
+2. **Fixed Agent JSON Input Status**:
+   ```markdown
+   | `agent` | @link-assistant/agent | ✅ | ✅ | `grok`, `sonnet`, `haiku` |
+   ```
+
+3. **Added Gemini-specific Features Section**:
+   - Stream JSON format documentation
+   - Yolo mode (auto-approval) documentation
+   - Sandbox mode documentation
+   - Checkpointing support documentation
+   - Model configuration documentation
+
+4. **Updated Feature List**:
+   - Added `gemini` to the Multiple CLI Agents list
+   - Updated description to include Gemini CLI
+
+### Verification
+
+| Tool | JSON Output | JSON Input | Verified Source |
+|------|-------------|------------|-----------------|
+| claude | ✅ (stream-json) | ✅ (stream-json) | Code + README |
+| codex | ✅ | ❌ | Code analysis |
+| opencode | ✅ | ❌ | Code analysis |
+| qwen | ✅ (stream-json) | ✅ (stream-json) | Code + README |
+| agent | ✅ | ✅ | Code + upstream README |
+| gemini | ✅ (stream-json) | ❌ | Code + upstream README |
+
+## Lessons Learned
+
+1. **Documentation-Code Sync**: When adding new tools or capabilities, update documentation in the same commit/PR
+2. **Verification Process**: Cross-reference code configurations with upstream tool documentation
+3. **Case Studies**: Documenting the investigation helps prevent similar issues and provides institutional knowledge
+
+## Files Modified
+
+| File | Changes |
+|------|---------|
+| README.md | Added Gemini to table, fixed Agent JSON Input, added Gemini features section |
+| docs/case-studies/issue-15/README.md | This case study document |
+| docs/case-studies/issue-15/evidence-timeline.md | Investigation evidence and timeline |
+
+## References
+
+- [google-gemini/gemini-cli](https://github.com/google-gemini/gemini-cli) - Official Gemini CLI repository
+- [@link-assistant/agent](https://github.com/link-assistant/agent) - Agent CLI repository
+- [Gemini CLI Headless Mode](https://geminicli.com/docs/cli/headless/) - JSON output documentation
+- [Issue #15](https://github.com/link-assistant/agent-commander/issues/15) - Original issue report
+
+## Conclusion
+
+The documentation discrepancies were caused by documentation lag rather than technical issues. The actual code implementations were correct - only the README.md needed updating to accurately reflect the supported tools and their capabilities.
+
+Key insight: Maintaining accurate documentation requires systematic verification against both the codebase and upstream tool capabilities. Creating case studies for such investigations helps prevent similar issues and provides a reference for future contributors.