Remove redundant docs directories

README.md

@@ -135,7 +135,7 @@ egg can run as a GitHub Action for CI/CD automation:
     anthropic-oauth-token: ${{ secrets.ANTHROPIC_OAUTH_TOKEN }}
 ```
 
-Trigger egg via @mentions in issues and PRs, or run it on any GitHub Actions event. See the [GitHub Action documentation](docs/features/github-action.md) and [@mention trigger setup guide](docs/guides/mention-trigger-setup.md) for details.
+Trigger egg via @mentions in issues and PRs, or run it on any GitHub Actions event. See the [GitHub Action documentation](action/README.md) and the [GitHub Actions ADR](docs/adr/in-progress/ADR-GitHub-Actions-Support.md) for details.
 
 ## CLI Reference
 
@@ -160,10 +160,8 @@ Trigger egg via @mentions in issues and PRs, or run it on any GitHub Actions eve
 
 - [Documentation Index](docs/index.md) - Navigation hub for all docs
 - [Architecture](docs/architecture/README.md) - System design and component overview
-- [Setup Guide](docs/setup/README.md) - First-time setup and configuration
-- [GitHub Action](docs/features/github-action.md) - CI/CD integration
-- [@mention Trigger Setup](docs/guides/mention-trigger-setup.md) - GitHub @mention automation
-- [Troubleshooting](docs/troubleshooting/) - Common issues and solutions
+- [Contributing](CONTRIBUTING.md) - Development setup and workflow
+- [GitHub Action](action/README.md) - CI/CD integration
 
 ### Component Documentation
 

action/README.md

@@ -26,6 +26,6 @@ This action runs the egg autonomous coding agent within GitHub Actions. It sets
 
 ## Documentation
 
-For full usage documentation including all inputs, outputs, examples, and security considerations, see the [GitHub Action feature documentation](../docs/features/github-action.md).
+For design details, inputs, outputs, and implementation notes, see the [GitHub Actions Support ADR](../docs/adr/in-progress/ADR-GitHub-Actions-Support.md).
 
-For setting up @mention triggers, see the [@mention trigger setup guide](../docs/guides/mention-trigger-setup.md).
+For the existing @mention trigger workflow, see [`.github/workflows/on-mention.yml`](../.github/workflows/on-mention.yml) and [`build-mention-prompt.sh`](build-mention-prompt.sh).

config/README.md

@@ -97,7 +97,7 @@ Egg supports separate tokens for writable and readable repositories:
 | `GITHUB_TOKEN` | Token for writable repos (or use GitHub App for auto-refresh) |
 | `GITHUB_READONLY_TOKEN` | Separate PAT for read-only repos (optional, falls back to `GITHUB_TOKEN`) |
 
-Using a separate read-only token provides security benefits. See [GitHub App Setup](../docs/setup/github-app-setup.md) for details.
+Using a separate read-only token provides security benefits. GitHub App setup is covered in `./setup.py` and the ADRs.
 
 ## repositories.yaml (Source of Truth for Repo Access)
 

config/secrets.template.env

@@ -44,7 +44,7 @@ SLACK_APP_TOKEN=""
 # 1. GITHUB_TOKEN - For writable repos (full access)
 #    Create a fine-grained token at https://github.com/settings/tokens?type=beta
 #    Required permissions: Contents (R/W), Pull requests (R/W), Workflows (R)
-#    OR configure a GitHub App (recommended) - see docs/setup/github-app-setup.md
+#    OR configure a GitHub App (recommended) - run ./setup.py for guided setup
 #
 # 2. GITHUB_READONLY_TOKEN - For read-only repos (optional)
 #    Used when monitoring repos where egg doesn't have write access

docs/README.md

@@ -6,34 +6,11 @@ Complete documentation for egg: a hardened sandbox for autonomous LLM code agent
 
 ## Documentation Structure
 
-### [Setup](setup/)
-Installation and configuration guides.
-
-- **[Setup Overview](setup/README.md)** - Quick start and prerequisites
-- **[GitHub App Setup](setup/github-app-setup.md)** - GitHub App permissions and installation
-- **[GitHub Auth Comparison](setup/github-auth-comparison.md)** - Auth method options
-
 ### [Architecture](architecture/)
 System design and technical details.
 
 - **[Overview](architecture/README.md)** - Gateway + sandbox architecture
 
-### [Features](features/)
-Feature documentation and capabilities.
-
-- **[Container Infrastructure](features/container-infrastructure.md)** - Container management and development environment
-- **[GitHub Action](features/github-action.md)** - Running egg in GitHub Actions CI/CD
-
-### [Guides](guides/)
-How-to guides for specific tasks.
-
-- **[@mention Trigger Setup](guides/mention-trigger-setup.md)** - Trigger egg via GitHub @mentions
-
-### [Reference](reference/)
-Quick reference guides.
-
-- **[Log Persistence](reference/log-persistence.md)** - Container log persistence and correlation
-
 ### [Development](development/)
 For contributors and developers.
 
@@ -46,16 +23,6 @@ Architecture Decision Records.
 - **[ADR Index](adr/README.md)** - All decisions and their status
 - **[Autonomous Software Engineer](adr/in-progress/ADR-Autonomous-Software-Engineer.md)** - Main system architecture
 
-### [Troubleshooting](troubleshooting/)
-Common issues and solutions.
-
-- **[GitHub Auth Issues](troubleshooting/github-auth-in-long-running-containers.md)** - Token expiry and refresh
-
-### [Plans](plans/)
-Implementation plans for future work.
-
-- **[GitHub Actions Implementation](plans/github-actions-implementation-plan.md)** - GitHub Actions integration plan
-
 ## Component READMEs
 
 Each component directory contains its own README with detailed documentation:
@@ -71,7 +38,6 @@ Each component directory contains its own README with detailed documentation:
 
 **Getting Started:**
 1. [Main README](../README.md) - Project overview
-2. [Setup Overview](setup/README.md) - Installation and configuration
 
 **Understanding the System:**
 1. [Architecture Overview](architecture/README.md) - Component design