Implement diagnostic checks for doctor command

[rrrodzilla]

Context

The doctor command currently only prints placeholder text but doesn't implement any actual diagnostic checks described in its documentation.

Location: src/commands/doctor.rs:52

Current Behavior

When running crately doctor:

Running system diagnostics...

Diagnostics to be implemented:
  - Configuration file validation
  - Database connectivity check
  - File system permissions
  - Dependency verification
  - Runtime environment checks

Doctor diagnostics complete

Expected Behavior

The doctor command should perform comprehensive health checks and report the status of each:

Running system diagnostics...

Configuration File............... ✓ Valid (~/.config/crately/config.toml)
Database Connectivity............ ✓ Connected (rocksdb://~/.local/share/crately/db)
OpenAI API Key................... ✓ Configured and valid
Cache Directory.................. ✓ Writable (~/.cache/crately)
Data Directory................... ✓ Writable (~/.local/share/crately)
Logs Directory................... ✓ Writable (~/.local/share/crately/logs)
Required Dependencies............ ✓ All available

✓ All diagnostics passed - system is healthy

Next steps:
  - Run 'crately serve' to start the server

Implementation Requirements

Diagnostic Checks to Implement

1. Configuration File Validation

   • Check config file exists at XDG_CONFIG_HOME/crately/config.toml
   • Parse and validate config structure
   • Check all required fields present
   • Validate field values (e.g., port ranges, timeouts)
   • Report specific issues if invalid

2. Database Connectivity Check

   • Verify database path is accessible
   • Test connection to embedded SurrealDB
   • Check database schema is initialized
   • Verify tables exist (crate, doc_chunk, embedding)
   • Check database is not locked by another process

3. File System Permissions

   • XDG_CONFIG_HOME/crately - readable/writable
   • XDG_DATA_HOME/crately - readable/writable
   • XDG_CACHE_HOME/crately - readable/writable
   • XDG_DATA_HOME/crately/logs - readable/writable
   • Database directory - readable/writable

4. Dependency Verification

   • OpenAI API key present (env var or config)
   • API key is valid (test API call if --verbose)
   • Network connectivity (if --verbose)
   • Required Rust version (cargo --version)

5. Runtime Environment Checks

   • Operating system and version
   • Available disk space in cache/data directories
   • Memory available
   • CPU architecture

Verbose Mode

When --verbose flag is used, show additional details:

Configuration File............... ✓ Valid
  Location: /home/user/.config/crately/config.toml
  Size: 1.2 KB
  Last modified: 2025-01-15 10:30:00
  Port: 3000
  Model: text-embedding-3-small

Database Connectivity............ ✓ Connected
  Type: RocksDB
  Location: /home/user/.local/share/crately/db
  Size: 45.2 MB
  Tables: 3 (crate, doc_chunk, embedding)
  Records: 1,234 chunks, 987 embeddings

OpenAI API Key................... ✓ Valid
  Source: Environment variable OPENAI_API_KEY
  Model: text-embedding-3-small (validated)

Error Reporting

When checks fail, provide actionable guidance:

Configuration File............... ✗ Invalid

  Error: Missing required field 'api_endpoint'
  
  To fix:
    1. Edit ~/.config/crately/config.toml
    2. Add: api_endpoint = "https://api.openai.com/v1/embeddings"
    3. Or run: crately init

Database Connectivity............ ✗ Failed

  Error: Database locked by another process (PID: 12345)
  
  To fix:
    1. Stop other crately instances: pkill crately
    2. Or use a different database path in config

Files to Modify

• src/commands/doctor.rs - Main implementation
• src/actors/config.rs - May need validation helpers
• src/database.rs - May need connectivity check functions
• CLAUDE.md - Update documentation

Implementation Pattern

pub fn run(args: DoctorArgs) -> Result<()> {
    println!("Running system diagnostics...\n");
    
    let mut all_passed = true;
    
    // Check 1: Configuration
    all_passed &= check_configuration(&args)?;
    
    // Check 2: Database
    all_passed &= check_database(&args)?;
    
    // Check 3: API Key
    all_passed &= check_api_key(&args)?;
    
    // Check 4: File permissions
    all_passed &= check_file_permissions(&args)?;
    
    // Check 5: Dependencies
    all_passed &= check_dependencies(&args)?;
    
    if all_passed {
        println!("\n✓ All diagnostics passed - system is healthy");
    } else {
        println!("\n✗ Some diagnostics failed - see details above");
        std::process::exit(1);
    }
    
    Ok(())
}

fn check_configuration(args: &DoctorArgs) -> Result<bool> {
    print!("Configuration File............... ");
    
    // Implementation here
    
    println!("✓ Valid");
    Ok(true)
}

Testing Requirements

• All diagnostic checks implemented
• Verbose mode shows additional details
• Failed checks exit with non-zero status
• Error messages are actionable
• --verbose and --fix flags work correctly
• All tests pass: cargo nextest run
• No clippy lints: cargo clippy --all-targets

Success Criteria

• All 5 diagnostic categories implemented
• Clear pass/fail indication for each check
• Actionable error messages with recovery steps
• Verbose mode provides detailed information
• Exit code reflects health status (0 = healthy, 1 = issues)
• Documentation updated

Related Files

• src/commands/doctor.rs - Main implementation needed (lines 52-58)
• src/actors/config.rs - Config validation
• CLAUDE.md - Documentation to update

Dependencies

This issue should be implemented before #74 (automatic fixes), as the fix logic will depend on the diagnostic checks.

Priority

Medium - Important for troubleshooting and system health verification