Add --run-log CLI flag to enable structured run logging without env var.
Print session directory path to stderr when run-log is enabled so Coding
Agents can easily locate log files for analysis.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Remove centralized skills.env.json5 in favor of per-skill .env files.
Clean up CredentialManager by removing hasEnv/getEnv/getResolvedEnvSnapshot
methods and skills env loading. Update CLI credentials and skills commands.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>