fix: resolve merge conflicts in github app config PR

[neverSettles]

Resolves conflicts between PR #1 and recent changes on main. Applies the github-app.pem path fix to the correct block in install.sh and integrates the new token chaining requirements in SKILL.md.

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EntelligenceAI PR Summary

This PR centralizes installation logic and enhances GitHub App authentication support by consolidating manual setup steps into a single external install script.

• Relocated GitHub App private key to dedicated config directory with automatic directory creation
• Refactored git identity configuration from environment variables to global git config commands with availability check
• Updated token precedence to prioritize GH_TOKEN over GITHUB_TOKEN in authentication setup
• Simplified Terraform bootstrap script by replacing ~40 lines of manual setup with external install script
• Added GitHub App environment variables (GITHUB_APP_ID, GITHUB_APP_INSTALLATION_ID, GITHUB_APP_PEM_PATH) and SETUP_TAILSCALE flag
• Removed manual git cloning, symlink creation, JSON config generation, and systemctl service management from user-data script

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Confidence Score: 5/5 - Safe to Merge

• No review comments were generated, indicating the code meets quality standards
• No critical, significant, or high-risk issues identified by automated analysis
• Good file coverage with 3 out of 4 changed files reviewed
• No existing unresolved comments that would block merging

[entelligence-ai-pr-reviews]

Walkthrough

This PR refactors the installation and configuration architecture to centralize setup logic and improve GitHub App authentication support. The main change consolidates manual installation steps into a single external install script, reducing the Terraform user-data script from ~40 lines to a simple script invocation. Configuration file organization is improved by relocating the GitHub App private key to a dedicated config directory. Git identity configuration is modernized by replacing environment variable exports with global git config commands, with automatic handling by the refresh script. GitHub token precedence is updated to prioritize GH_TOKEN over GITHUB_TOKEN, and new environment variables support GitHub App authentication.

Changes

File(s)	Summary
install.sh	Relocated GitHub App private key file from installation directory to dedicated config directory; added mkdir -p command to ensure $CONFIG_DIR exists before copying PEM file.
scripts/refresh-github-token.sh	Refactored git identity configuration from environment variable exports (GIT_AUTHOR_NAME, GIT_AUTHOR_EMAIL, GIT_COMMITTER_NAME, GIT_COMMITTER_EMAIL) to git config --global commands for user.name and user.email; added safety check to verify git command availability; consolidated four identity settings into two commands.
skills/proactive-engineer/SKILL.md	Updated GitHub token authentication to prioritize GH_TOKEN over GITHUB_TOKEN; removed explicit git config commands for user.name and user.email as refresh script now handles identity configuration automatically.
terraform/user-data.sh	Replaced ~40 lines of manual installation logic with single external install script call; added GitHub App environment variables (GITHUB_APP_ID, GITHUB_APP_INSTALLATION_ID, GITHUB_APP_PEM_PATH) and SETUP_TAILSCALE flag; removed manual git cloning, symlink creation, JSON config generation, and systemctl service management.

Sequence Diagram

This diagram shows the interactions between components:

sequenceDiagram
    participant Script as Installation Script
    participant FS as File System
    participant Env as Environment

    Script->>Script: Check USE_GITHUB_APP = "yes"
    Script->>Script: Check GITHUB_APP_PEM_PATH is set
    
    alt GitHub App authentication enabled
        Note over Script,FS: New: Ensure config directory exists
        Script->>FS: mkdir -p $CONFIG_DIR
        FS-->>Script: Directory created/verified
        
        Script->>Script: Set PEM_DEST=$CONFIG_DIR/github-app.pem
        
        Script->>FS: Copy PEM file from GITHUB_APP_PEM_PATH to PEM_DEST
        FS-->>Script: File copied
        
        Script->>FS: chmod 600 on PEM_DEST
        FS-->>Script: Permissions set
        
        Script->>Env: Export GITHUB_APP_PEM_PATH=PEM_DEST
        Env-->>Script: Variable exported
    else GitHub App not used
        Note over Script: Skip GitHub App setup
    end

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[neverSettles]

I attempted to resolve the merge conflicts locally but ran into auth issues when trying to push the resolved branch back up to origin/fix/github-app-config-and-docs. Could a maintainer pull this down, resolve the user-data.sh conflict, and force push?