# Troubleshooting Guide

Common issues and solutions when using omni-dev.

## Table of Contents

1. [Installation Issues](#installation-issues)
2. [API Key Problems](#api-key-problems)
3. [Configuration Issues](#configuration-issues)
4. [Commit Analysis Problems](#commit-analysis-problems)
5. [Performance Issues](#performance-issues)
6. [Git Repository Issues](#git-repository-issues)
7. [Command Line Issues](#command-line-issues)
8. [Atlassian Integration Issues](#atlassian-integration-issues)
9. [Datadog Integration Issues](#datadog-integration-issues)
10. [MCP Server Issues](#mcp-server-issues)
11. [`claude-cli` Backend Issues](#claude-cli-backend-issues)
12. [Getting Help](#getting-help)

## Installation Issues

### Error: `cargo install omni-dev` fails

**Symptom**: Installation fails with compilation errors.

**Common Causes & Solutions**:

1. **Rust Version Too Old**

   ```bash
   # Check Rust version
   rustc --version
   
   # Update Rust (need 1.80+)
   rustup update
   ```

2. **Missing System Dependencies**

   ```bash
   # macOS
   xcode-select --install
   
   # Ubuntu/Debian
   sudo apt update
   sudo apt install build-essential pkg-config libssl-dev
   
   # CentOS/RHEL
   sudo yum groupinstall "Development Tools"
   sudo yum install openssl-devel
   ```

3. **Network Issues**

   ```bash
   # Use alternative registry
   cargo install omni-dev --registry crates-io
   
   # Or build from source
   git clone https://github.com/rust-works/omni-dev.git
   cd omni-dev
   cargo build --release
   ```

### Error: `omni-dev: command not found`

**Symptom**: Command not found after installation.

**Solution**: Add Cargo bin directory to PATH:

```bash
# Add to your shell profile (.bashrc, .zshrc, etc.)
export PATH="$HOME/.cargo/bin:$PATH"

# Reload shell or run:
source ~/.bashrc  # or ~/.zshrc
```

## API Key Problems

> For first-time setup, see
> [Authentication](configuration.md#authentication). The errors below
> cover failure modes after setup.

### Error: `CLAUDE_API_KEY not found`

**Symptom**:

```
Error: Claude API key not found
  Caused by: API key not found
```

**Solutions**:

1. **Set Environment Variable**

   The Anthropic backend accepts any of `CLAUDE_API_KEY`,
   `ANTHROPIC_API_KEY`, or `ANTHROPIC_AUTH_TOKEN` (first match wins).

   ```bash
   export CLAUDE_API_KEY="your-api-key-here"
   
   # Make permanent
   echo 'export CLAUDE_API_KEY="your-key"' >> ~/.bashrc
   source ~/.bashrc
   ```

2. **Verify Key Format**

   ```bash
   # Should start with "sk-ant-api03-"
   echo $CLAUDE_API_KEY | head -c 20
   ```

3. **Check for Hidden Characters**

   ```bash
   # Remove whitespace/newlines
   export CLAUDE_API_KEY="$(echo $CLAUDE_API_KEY | tr -d '[:space:]')"
   ```

### Error: `API request failed: HTTP 401`

**Symptom**: Authentication failed.

**Causes & Solutions**:

1. **Invalid API Key**
   - Get new key from [Anthropic Console](https://console.anthropic.com/)
   - Ensure key is active and not expired

2. **Wrong Key Format**

   ```bash
   # API key should look like:
   sk-ant-api03-abcd1234...
   ```

3. **Account Issues**
   - Check account status at Anthropic Console
   - Ensure billing/credits are available

### Error: `API request failed: HTTP 429`

**Symptom**: Rate limited.

**Solutions**:

1. **Reduce Concurrency**

   ```bash
   # Lower parallel requests
   omni-dev git commit message twiddle 'HEAD~10..HEAD' --concurrency 1
   ```

2. **Wait and Retry**
   - Wait a few minutes between large requests
   - Rate limits reset over time

3. **Upgrade API Tier**
   - Check rate limits in Anthropic Console
   - Consider upgrading account tier

## Configuration Issues

### Error: Scopes not detected

**Symptom**: omni-dev doesn't use project-specific scopes.

**Debugging Steps**:

1. **Check Directory Structure**

   ```bash
   ls -la .omni-dev/
   # Should show: scopes.yaml, commit-guidelines.md
   ```

2. **Validate YAML Syntax**

   ```bash
   # Check YAML is valid
   python -c "import yaml; yaml.safe_load(open('.omni-dev/scopes.yaml'))"
   
   # Or use online YAML validator
   ```

3. **Test File Patterns**

   ```bash
   # See what files changed in commit
   git show --name-only HEAD
   
   # Check if patterns match
   grep -A5 "file_patterns" .omni-dev/scopes.yaml
   ```

4. **Use Absolute Context Directory**

   ```bash
   # Specify full path
   omni-dev git commit message twiddle 'HEAD~3..HEAD' --context-dir "$(pwd)/.omni-dev"
   ```

### Error: Context directory not found

**Symptom**:

```
Context directory not found: .omni-dev/
```

**Solutions**:

1. **Create Directory**

   ```bash
   mkdir .omni-dev
   ```

2. **Check Current Directory**

   ```bash
   # Must be in git repository root
   pwd
   git rev-parse --show-toplevel  # Should match
   ```

3. **Use Custom Directory**

   ```bash
   # If config is elsewhere
   omni-dev git commit message twiddle 'HEAD~3..HEAD' --context-dir ./config
   ```

### Error: YAML parsing failed

**Symptom**: Configuration file syntax errors.

**Solutions**:

1. **Check YAML Syntax**

   ```bash
   # Common issues:
   # - Tabs instead of spaces
   # - Missing quotes around strings with special chars
   # - Incorrect indentation
   
   # Validate with Python
   python -c "import yaml; print(yaml.safe_load(open('.omni-dev/scopes.yaml')))"
   ```

2. **Fix Common Issues**

   ```yaml
   # ❌ Bad - tabs used
   scopes:
    - name: "api"
   
   # ✅ Good - spaces used
   scopes:
     - name: "api"
   
   # ❌ Bad - unquoted string with colon
   - name: api: endpoints
   
   # ✅ Good - quoted string
   - name: "api: endpoints"
   ```

## Commit Analysis Problems

### Error: `Not in a git repository`

**Symptom**:

```
Error: Failed to open git repository
  Caused by: Not in a git repository
```

**Solutions**:

1. **Check Git Repository**

   ```bash
   git status  # Should work
   
   # If not a git repo:
   git init
   ```

2. **Check Working Directory**

   ```bash
   # Must be inside git repository
   cd /path/to/your/git/repo
   omni-dev git commit message twiddle 'HEAD~3..HEAD'
   ```

### Error: `Working directory is not clean`

**Symptom**:

```
Error: Cannot amend commits with uncommitted changes
  Caused by: Working directory is not clean
```

**Solutions**:

1. **Commit Changes**

   ```bash
   git add .
   git commit -m "temp commit"
   ```

2. **Stash Changes**

   ```bash
   git stash push -m "temp stash"
   # After omni-dev: git stash pop
   ```

3. **Use View Instead of Twiddle**

   ```bash
   # View doesn't require clean directory
   omni-dev git commit message view 'HEAD~3..HEAD'
   ```

### Error: Invalid commit range

**Symptom**:

```
Error: Invalid commit range: HEAD~100..HEAD
```

**Solutions**:

1. **Check Available Commits**

   ```bash
   # See how many commits exist
   git log --oneline | wc -l
   ```

2. **Use Valid Range**

   ```bash
   # If only 5 commits exist:
   omni-dev git commit message twiddle 'HEAD~5..HEAD'
   
   # Or use specific hashes:
   omni-dev git commit message twiddle 'abc123..def456'
   ```

3. **Check Branch History**

   ```bash
   git log --oneline -10  # See recent commits
   ```

### Error: No commits found in range

**Symptom**: Empty commit range or no commits to analyze.

**Solutions**:

1. **Verify Commit Range**

   ```bash
   # Check what's in range
   git log --oneline 'HEAD~3..HEAD'
   ```

2. **Use Different Range**

   ```bash
   # Compare to main branch
   omni-dev git commit message twiddle 'origin/main..HEAD'
   
   # Or use absolute range
   omni-dev git commit message twiddle 'HEAD~5..HEAD'
   ```

## Performance Issues

### Issue: Slow processing with large commit ranges

**Symptom**: omni-dev takes a long time with many commits.

**Solutions**:

1. **Reduce Concurrency**

   ```bash
   # Lower parallel requests
   omni-dev git commit message twiddle 'HEAD~20..HEAD' --concurrency 2
   ```

2. **Process in Stages**

   ```bash
   # Break up large ranges
   omni-dev git commit message twiddle 'HEAD~10..HEAD~5'
   omni-dev git commit message twiddle 'HEAD~5..HEAD'
   ```

3. **Save and Review**

   ```bash
   # Save suggestions first, then apply
   omni-dev git commit message twiddle 'HEAD~20..HEAD' --save-only suggestions.yaml
   omni-dev git commit message amend suggestions.yaml
   ```

### Issue: API timeouts

**Symptom**: Requests timing out or failing.

**Solutions**:

1. **Reduce Concurrency**

   ```bash
   omni-dev git commit message twiddle 'HEAD~10..HEAD' --concurrency 1
   ```

2. **Retry with Exponential Backoff**

   ```bash
   # Wait between retries
   sleep 30
   omni-dev git commit message twiddle 'HEAD~5..HEAD'
   ```

## Git Repository Issues

### Error: Cannot amend non-HEAD commits

**Symptom**: Trying to amend commits that aren't the latest.

**Expected Behavior**: omni-dev uses interactive rebase for non-HEAD commits.

**If Problems Occur**:

1. **Ensure Clean Working Directory**

   ```bash
   git status  # Should be clean
   ```

2. **Check Interactive Rebase Setup**

   ```bash
   # Set git editor if needed
   git config --global core.editor "nano"
   # or vim, code --wait, etc.
   ```

3. **Manual Rebase if Needed**

   ```bash
   # Do interactive rebase manually
   git rebase -i HEAD~5
   # Edit commit messages as needed
   ```

### Error: Remote branch not found

**Symptom**: Can't find origin/main or base branch, or commands report
`No default base branch found (checked origin/main, origin/master, main, master)`.

When no commit range or base branch is given, `git commit message check` and
`git branch info` resolve the default base remote-first: `origin/main`, then
`origin/master`, then local `main`, then local `master`. If none of these
refs exist, they error rather than guessing a range.

**Solutions**:

1. **Check Remote Branches**

   ```bash
   git branch -r  # See remote branches
   ```

2. **Update Remote References**

   ```bash
   git fetch origin
   ```

3. **Use Correct Branch Name**

   ```bash
   # If main branch is 'master':
   omni-dev git commit message twiddle 'origin/master..HEAD'
   ```

### Error: Merge conflicts during rebase

**Symptom**: Interactive rebase fails with conflicts.

**Solutions**:

1. **Resolve Conflicts Manually**

   ```bash
   # Edit conflicted files
   git add .
   git rebase --continue
   ```

2. **Abort and Try Different Approach**

   ```bash
   git rebase --abort
   
   # Use smaller commit ranges
   omni-dev git commit message twiddle 'HEAD~3..HEAD'
   ```

## Command Line Issues

### Error: Unknown argument

**Symptom**:

```
error: unexpected argument '--unknown-flag' found
```

**Solutions**:

1. **Check Available Options**

   ```bash
   omni-dev git commit message twiddle --help
   ```

2. **Use Correct Flag Names**

   ```bash
   # Common correct flags:
   --use-context
   --concurrency 4
   --no-coherence
   --auto-apply
   --save-only file.yaml
   --context-dir ./config
   ```

### Error: Invalid commit range format

**Symptom**: Git range syntax errors.

**Valid Formats**:

```bash
# ✅ Valid ranges:
'HEAD~5..HEAD'          # Last 5 commits
'origin/main..HEAD'     # Current branch vs main
'abc123..def456'        # Between specific commits
'HEAD^..HEAD'           # Just last commit

# ❌ Invalid:
HEAD~5..HEAD           # Missing quotes
'HEAD-5..HEAD'         # Wrong syntax (-5 instead of ~5)
'HEAD..HEAD~5'         # Backwards range
```

### Issue: Quotes and Shell Escaping

**Symptom**: Shell interpreting range characters incorrectly.

**Solutions**:

```bash
# ✅ Always quote commit ranges:
omni-dev git commit message twiddle 'HEAD~5..HEAD'

# ✅ Or escape special characters:
omni-dev git commit message twiddle HEAD~5..HEAD

# On Windows Command Prompt:
omni-dev git commit message twiddle "HEAD~5..HEAD"
```

## Atlassian Integration Issues

### Error: `Atlassian: missing instance URL / email / API token`

**Cause**: omni-dev cannot find Atlassian credentials in the environment or
in `~/.omni-dev/settings.json`.

**Solution**:

```bash
# Run interactive setup
omni-dev atlassian auth login

# Or export environment variables (override the settings file)
export ATLASSIAN_INSTANCE_URL=https://myorg.atlassian.net
export ATLASSIAN_EMAIL=you@example.com
export ATLASSIAN_API_TOKEN=...

# Verify
omni-dev atlassian auth status
```

API tokens are issued at <https://id.atlassian.com/manage-profile/security/api-tokens>.
Note: Atlassian API tokens are scoped to the email account and the instance
URL — copy them carefully and avoid trailing whitespace.

### Error: `404 Not Found` on a known JIRA key or Confluence page

Almost always one of:

1. **Wrong instance URL.** Check `ATLASSIAN_INSTANCE_URL` matches the
   Atlassian Cloud site that contains the resource.
2. **Permission.** Your account does not have read access to the project /
   space.
3. **Trailing slash.** `omni-dev atlassian auth login` strips them, but if
   you set `ATLASSIAN_INSTANCE_URL` manually, ensure no trailing slash.

### MCP `jira_*` / `confluence_*` tools fail with auth errors

The MCP server inherits the environment of whatever launched it (Claude
Desktop, Claude Code, the Inspector). If you exported credentials in your
shell after launching the client, restart the client. Run the
`atlassian_auth_status` MCP tool to confirm what the server sees.

## Datadog Integration Issues

### Error: `Datadog: missing API key / APP key`

**Cause**: Datadog requires both keys (an API key authenticates the source,
an APP key scopes the user). Missing either fails.

```bash
# Interactive
omni-dev datadog auth login

# Environment variables (override the settings file)
export DATADOG_API_KEY=...
export DATADOG_APP_KEY=...
export DATADOG_SITE=datadoghq.com   # or datadoghq.eu, us3.datadoghq.com, etc.

# Verify
omni-dev datadog auth status
```

### Error: `403 Forbidden` from a Datadog endpoint

The site is wrong. Datadog accounts are bound to a region; an EU account
will return 403 against `datadoghq.com`. Check the URL of the Datadog UI you
log into in the browser:

| Browser URL host          | `DATADOG_SITE`        |
|---------------------------|-----------------------|
| `app.datadoghq.com`       | `datadoghq.com` (default) |
| `app.datadoghq.eu`        | `datadoghq.eu`        |
| `app.us3.datadoghq.com`   | `us3.datadoghq.com`   |
| `app.us5.datadoghq.com`   | `us5.datadoghq.com`   |
| `app.ap1.datadoghq.com`   | `ap1.datadoghq.com`   |
| `app.ddog-gov.com`        | `ddog-gov.com`        |

For on-prem / proxied installs, set `DATADOG_API_URL` to the full base URL
(it overrides the site-derived URL entirely).

### Error: `429 Too Many Requests`

omni-dev honours `Retry-After` and Datadog's `X-RateLimit-Reset` headers.
When retries are exhausted, the error message includes the rate-limit
headers so you can see the window. Either back off and retry, or split your
query into smaller windows.

## MCP Server Issues

### Error: `omni-dev-mcp: command not found`

The default `cargo install omni-dev` does **not** install the MCP server.
Re-install with the feature flag:

```bash
cargo install omni-dev --features mcp
```

### Error: `failed to open git repository`

The MCP server uses its own working directory when tools that need a git
repo are called without an explicit `repo_path`. The assistant launched
the server from somewhere outside your repo (commonly the user home).

Either configure the server to launch from the repo (Claude Code's
`.mcp.json` at the repo root does this automatically), or pass `repo_path`
to each git tool call.

### Tools list as expected but never return / hang

Use the MCP Inspector to bypass the assistant and rule out a client-side
issue:

```bash
npx @modelcontextprotocol/inspector omni-dev-mcp
```

If the Inspector also hangs, run with verbose logs:

```bash
RUST_LOG=debug omni-dev-mcp
RUST_LOG=omni_dev::mcp=trace omni-dev-mcp
```

Logs go to **stderr** because stdin/stdout are reserved for MCP framing.

## `claude-cli` Backend Issues

See the [AI Backends Guide](ai-backends.md) for setup, sandbox semantics, and
the full inventory of `OMNI_DEV_CLAUDE_CLI_*` knobs. The cases below cover
the most common runtime errors.

### Error: `the assistant tried to use a tool but tools are disabled`

The `claude-cli` backend runs the nested Claude session with `--tools ""`
by default. If your prompt requires tool use, opt in with the escape hatch:

```bash
export OMNI_DEV_CLAUDE_CLI_ALLOW_TOOLS=true
# or pass --claude-cli-allow-tools
```

A WARN is logged every time the escape hatch is active.

### Error: `MCP server X not loaded`

The backend also passes `--strict-mcp-config` by default, which suppresses
all MCP servers from `~/.claude/settings.json`. Opt in with:

```bash
export OMNI_DEV_CLAUDE_CLI_ALLOW_MCP=true
# or pass --claude-cli-allow-mcp
```

Independent of the tool escape hatch — combine or use separately.

### Error: `claude -p exited with cost cap exceeded`

You set a per-invocation cap and the nested session went past it:

```bash
export OMNI_DEV_CLAUDE_CLI_MAX_BUDGET_USD=2.50
# or --claude-cli-max-budget-usd 2.50
```

omni-dev logs `total_cost_usd` from every invocation at INFO level — review
the logs to size the cap appropriately, then re-run.

### AI scratch directory growing

Both the default and `claude-cli` backends spool large artefacts to
`~/.cache/omni-dev/ai-scratch/`. The directory is not purged automatically
(yet). Safe to delete manually between runs.

## Getting Help

### Enable Debug Output

omni-dev uses the standard Rust logging system via the `RUST_LOG` environment variable. This provides detailed diagnostic information for troubleshooting.

#### Basic Usage

```bash
# Enable debug output for all omni-dev components
RUST_LOG=omni_dev=debug omni-dev git commit message twiddle 'HEAD~3..HEAD' --use-context

# Enable all debug logging (including dependencies)
RUST_LOG=debug omni-dev git commit message twiddle 'HEAD~3..HEAD'

# Only show errors and warnings
RUST_LOG=warn omni-dev git commit message twiddle 'HEAD~3..HEAD'
```

#### Log Levels (in order of verbosity)

- `error` - Only errors
- `warn` - Warnings and errors (default)  
- `info` - Informational messages + above
- `debug` - Debug information + above
- `trace` - Most verbose logging + above

#### Module-Specific Logging

Target specific components for focused debugging:

```bash
# Debug only context discovery
RUST_LOG=omni_dev::claude::context::discovery=debug omni-dev git commit message twiddle ...

# Debug only Claude API interactions
RUST_LOG=omni_dev::claude::client=debug omni-dev git commit message twiddle ...

# Debug only CLI processing
RUST_LOG=omni_dev::cli=debug omni-dev git commit message twiddle ...

# Multiple modules
RUST_LOG=omni_dev::claude=debug,omni_dev::git=info omni-dev git commit message twiddle ...
```

#### Common Debugging Scenarios

**Configuration Issues:**
```bash
# See what config files are loaded
RUST_LOG=omni_dev::claude::context::discovery=debug omni-dev git commit message twiddle ...
```

**API Communication Problems:**
```bash  
# Debug Claude API calls
RUST_LOG=omni_dev::claude::client=debug omni-dev git commit message twiddle ...
```

**YAML Parsing Errors:**
```bash
# See raw Claude responses and parsing details
RUST_LOG=omni_dev::claude=debug omni-dev git commit message twiddle ...
```

#### Output Format

Debug output includes:
- **Timestamp** - When the event occurred
- **Level** - Log level (DEBUG, INFO, etc.)
- **Module** - Which component generated the log
- **Message** - The log message with structured fields
- **Context** - Additional structured data (file paths, sizes, etc.)

Example output:
```
2025-09-09T14:42:46.673223Z DEBUG omni_dev::claude::context::discovery: Looking for context directory context_dir="./.omni-dev" exists=true
2025-09-09T14:42:46.673282Z DEBUG omni_dev::claude::context::discovery: Loaded commit guidelines bytes=1449
```

### Collect System Information

When reporting issues, include:

```bash
# System info
uname -a
rustc --version
cargo --version

# Git info  
git --version
git status
git log --oneline -5

# omni-dev info
omni-dev --version

# Configuration
ls -la .omni-dev/
echo "API key length: $(echo $CLAUDE_API_KEY | wc -c)"
```

### Test with Minimal Example

Create a minimal reproduction:

```bash
# Create test repo
mkdir test-omni-dev
cd test-omni-dev
git init

# Create test commits
echo "first" > file.txt
git add file.txt
git commit -m "first commit"

echo "second" > file.txt
git add file.txt  
git commit -m "second commit"

# Test omni-dev
omni-dev git commit message twiddle 'HEAD^..HEAD' --use-context
```

### Common Solutions Checklist

Before asking for help, verify:

- [ ] omni-dev is latest version: `cargo install omni-dev`
- [ ] CLAUDE_API_KEY is set correctly
- [ ] In a git repository: `git status` works
- [ ] Working directory is clean (for twiddle command)
- [ ] Commit range is valid: `git log --oneline 'HEAD~5..HEAD'`
- [ ] Configuration syntax is correct (if using `.omni-dev/`)

## Support Channels

### GitHub Issues

For bugs and feature requests: <https://github.com/rust-works/omni-dev/issues>

**Include in Bug Reports**:

- omni-dev version: `omni-dev --version`
- Rust version: `rustc --version`  
- Operating system
- Complete error message
- Steps to reproduce
- Minimal example if possible

### GitHub Discussions  

For questions and general help: <https://github.com/rust-works/omni-dev/discussions>

### Community Support

- Tag questions with `omni-dev` on Stack Overflow
- Join Rust community channels and ask about Git tools

### Documentation

- [User Guide](user-guide.md) - Complete usage guide
- [Configuration Guide](configuration.md) - Setup instructions
- [Examples](examples.md) - Real-world examples

## Frequently Asked Questions

### Q: Can I use omni-dev without Claude API key?

**A**: No, the AI-powered features require a Claude API key. However, you
can use the `view` command to analyze commits without AI suggestions.

### Q: Does omni-dev modify my git history?

**A**: Only when you explicitly approve changes. The `view` command is
read-only. The `twiddle` command shows you proposed changes and asks for
confirmation before applying.

### Q: Can I undo changes made by omni-dev?

**A**: Yes, git tracks all changes:

```bash
# See recent changes
git reflog

# Undo last change
git reset --hard HEAD@{1}
```

### Q: Is it safe to use on shared/public repositories?

**A**: Yes, but be careful:

- Always review changes before applying
- Don't rewrite history on shared branches
- Consider using `--save-only` for review workflows

### Q: How much does the Claude API cost?

**A**: Check current pricing at
[Anthropic Pricing](https://anthropic.com/pricing). Typical usage for commit
message improvement is very low cost.

### Q: Can I use this in CI/CD pipelines?

**A**: Yes, but consider:

- Store API key as secure secret
- Use `--auto-apply` for automated workflows
- Test thoroughly in development first
- Be mindful of API rate limits
