Update readme's, branches and actions

SECURITY_PRIVATE_FILES.md

@@ -5,15 +5,17 @@ This document explains which files are kept private and why.
 ## Files Excluded from Git & Docker
 
 ### Deployment Documentation (Private)
+
 - `ADMIN_DEPLOYMENT_SUMMARY.md` - Internal deployment status and setup details
 - `CI_CD_PORTAINER_GUIDE.md` - Private CI/CD and Portainer configuration
 - `DEPLOYMENT.md` - Deployment procedures and configuration guidance
 - `GETTING_STARTED.md` - Internal setup instructions
-- `INTERNAL_*.md` - Any file prefixed with INTERNAL_ (pattern-based exclusion)
-- `SETUP_*.md` - Any file prefixed with SETUP_ (pattern-based exclusion)
-- `DEPLOY_*.md` - Any file prefixed with DEPLOY_ (pattern-based exclusion)
+- `INTERNAL_*.md` - Any file prefixed with INTERNAL\_ (pattern-based exclusion)
+- `SETUP_*.md` - Any file prefixed with SETUP\_ (pattern-based exclusion)
+- `DEPLOY_*.md` - Any file prefixed with DEPLOY\_ (pattern-based exclusion)
 
 ### Custom Instruction Files (Private)
+
 - `.instructions.md` - GitHub Copilot custom instructions
 - `.prompt.md` - Custom prompt templates
 - `.agent.md` - Custom agent definitions
@@ -22,26 +24,30 @@ This document explains which files are kept private and why.
 - `AGENTS.md` - Agent configuration
 
 These are kept private to prevent exposure of:
+
 - Development workflow details
 - Copilot customization strategies
 - Internal coding guidelines and preferences
 - Prompt engineering techniques
 
 ### Private Scripts
+
 - `scripts/private/` - Directory for private deployment scripts
 - `scripts/*.local.*` - Local-specific script configurations
 
 ## Files Included in Public Repo
 
 ### Public Documentation
+
 - `README.md` - Main project documentation
 - `DOCKER_README.md` - Docker usage documentation
 - `admin_ui/README.md` - Admin UI documentation
 - `admin_ui/SCHEDULE_API.md` - Public API documentation
 - `transit_api/README.md` - API documentation
-- `bus_terminal/README.md` - Flutter app documentation
+- `deprecated/README.md` - Legacy Flutter bus terminal documentation kept for historical reference
 
 ### Configuration
+
 - `.env.example` - Environment variable template (no secrets)
 - `.gitignore` - Git exclusion rules
 - `.dockerignore` - Docker build exclusion rules
@@ -49,13 +55,15 @@ These are kept private to prevent exposure of:
 - `Dockerfile` files - Container definitions
 
 ### Code & Configuration
-- All source code in `auth_api/`, `transit_api/`, `employee_api/`, `admin_ui/`, `bus_terminal/`
+
+- All source code in `auth_api/`, `transit_api/`, `employee_api/`, `admin_ui/`, and the legacy `deprecated/` app
 - `package.json` files (no secrets, only dependencies)
 - GitHub Actions workflows in `.github/workflows/`
 
 ## Environment Variables - NEVER Commit
 
 Always keep the following OUT of git:
+
 - `.env` - Local environment variables (in `.gitignore`)
 - Database credentials
 - JWT secrets
@@ -67,6 +75,7 @@ Use `.env.example` as a template and create local `.env` files for development.
 ## Docker Build Security
 
 All `.dockerignore` files (root and per-service) ensure that:
+
 1. Sensitive documentation never enters Docker images
 2. Private scripts and configs are excluded from builds
 3. Only necessary source code and dependencies are included
@@ -75,6 +84,7 @@ All `.dockerignore` files (root and per-service) ensure that:
 ## GitHub Actions Security
 
 The CI/CD workflow in `.github/workflows/docker-build.yml`:
+
 - Only builds from specific service directories (auth_api, transit_api, etc.)
 - Respects `.dockerignore` rules
 - Uses GitHub secrets for credentials (never hardcoded)
@@ -93,12 +103,14 @@ The CI/CD workflow in `.github/workflows/docker-build.yml`:
 To keep new private files out of the repo and Docker:
 
 1. Add pattern to `.gitignore`:
+
    ```
    MYFILE_*.md
    new_private_thing.*
    ```
 
 2. Add pattern to `.dockerignore` (root and per-service):
+
    ```
    /MYFILE_*.md
    /new_private_thing.*