docs: update README version references to 1.1.1, add missing documentation

Also clean up root directory structure:
- Merge pytest.ini and vulture.toml into pyproject.toml
- Consolidate .env.docker.example and .env.https into .env.example
- Move shell scripts (build-docker.sh, docker-run.sh, start_https.sh) to scripts/
- Move DOCKER.md to docs/
- Merge requirements-dev.txt into dev-requirements.txt
- Remove misplaced test file from package root
- Update all cross-references in README, docs, CI workflow, and scripts

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: ril3y

.dockerignore

@@ -62,7 +62,6 @@ dev_manager.log
 # Environment files (use docker-compose env)
 .env
 .env.local
-.env.https
 MakerMatrix/frontend/.env
 MakerMatrix/frontend/.env.local
 

.env.docker.example

@@ -2,36 +2,67 @@
 # Copy this file to .env and fill in your actual values
 # NEVER commit .env to git!
 
+# ── Core Settings ─────────────────────────────────────────────
+DEBUG=false
+LOG_LEVEL=INFO
+
+# Database
+DATABASE_URL=sqlite:///./makermatrix.db
+
+# Security (REQUIRED — change in production!)
+JWT_SECRET_KEY=your-secure-secret-key-here-change-this-in-production
+JWT_ACCESS_TOKEN_EXPIRE_MINUTES=480
+JWT_REFRESH_TOKEN_EXPIRE_DAYS=7
+
+# Server
+SERVER_HOST=localhost
+
+# CORS
+CORS_ORIGINS=http://localhost:3000,http://localhost:5173,http://localhost:5174,http://127.0.0.1:3000,http://127.0.0.1:5173,http://127.0.0.1:5174,*
+
+# Encryption Key for Credential Storage
+MAKERMATRIX_ENCRYPTION_KEY=your_encryption_key_here
+
 # MakerMatrix API Key (for testing/automation)
 # Generate via: POST /api/api-keys/ (requires admin authentication)
 MAKERMATRIX_API_KEY=
 
-# DigiKey API Credentials
-DIGIKEY_CLIENT_ID=your_digikey_client_id_here
-DIGIKEY_CLIENT_SECRET=your_digikey_client_secret_here
-# Set to True for sandbox testing, False for production
-DIGIKEY_CLIENT_SANDBOX=True
+# ── Supplier API Keys (Optional) ─────────────────────────────
+# DigiKey OAuth2
+DIGIKEY_CLIENT_ID=
+DIGIKEY_CLIENT_SECRET=
+# Set to true for sandbox testing, false for production
+DIGIKEY_CLIENT_SANDBOX=true
 
-# Encryption Key for Credential Storage
-MAKERMATRIX_ENCRYPTION_KEY=your_encryption_key_here
+# Mouser
+MOUSER_API_KEY=
 
-# Database Settings
-DATABASE_URL=sqlite:///./makermatrix.db
+# LCSC
+LCSC_API_KEY=
 
-# Development Settings
-DEBUG=False
-LOG_LEVEL=INFO
-# Set to false to run dev_manager in HTTP mode (default, no certificates required)
+# ── AI Configuration (Optional) ──────────────────────────────
+# Ollama (local or Docker host)
+OLLAMA_BASE_URL=http://host.docker.internal:11434
+
+# OpenAI
+OPENAI_API_KEY=
+
+# Anthropic
+ANTHROPIC_API_KEY=
+
+# ── HTTPS (Optional) ─────────────────────────────────────────
 # Set to true for HTTPS mode (requires certs/ directory with valid SSL certificates)
 HTTPS_ENABLED=false
+SSL_CERT_PATH=certs/cert.pem
+SSL_KEY_PATH=certs/key.pem
+HTTPS_PORT=8443
 
-# Security Settings
-JWT_SECRET_KEY=your-secure-secret-key-here-change-this-in-production
-JWT_ACCESS_TOKEN_EXPIRE_MINUTES=480
-JWT_REFRESH_TOKEN_EXPIRE_DAYS=7
+# HTTP
+HTTP_PORT=8080
+HTTP_REDIRECT_TO_HTTPS=true
 
-# Server Configuration
-SERVER_HOST=localhost
+# CORS Origins for HTTPS (uncomment and adjust if using HTTPS)
+# CORS_ORIGINS=https://localhost:8443,https://127.0.0.1:8443,http://localhost:8080
 
-# CORS Configuration
-CORS_ORIGINS=http://localhost:3000,http://localhost:5173,http://localhost:5174,http://127.0.0.1:3000,http://127.0.0.1:5173,http://127.0.0.1:5174,*
+# DigiKey OAuth Callback for HTTPS (uncomment if using HTTPS)
+# DIGIKEY_OAUTH_CALLBACK=https://localhost:8443/digikey_callback

.env.example

@@ -6,15 +6,15 @@ on:
     paths:
       - 'MakerMatrix/**/*.py'
       - 'tests/**/*.py'
-      - 'vulture.toml'
+      - 'pyproject.toml'
       - '.github/workflows/backend-quality.yml'
       - 'requirements.txt'
   pull_request:
     branches: [ main, develop ]
     paths:
       - 'MakerMatrix/**/*.py'
       - 'tests/**/*.py'
-      - 'vulture.toml'
+      - 'pyproject.toml'
       - '.github/workflows/backend-quality.yml'
       - 'requirements.txt'
   workflow_dispatch:
@@ -80,16 +80,16 @@ jobs:
     - name: Run Vulture dead code analysis
       run: |
         source venv_test/bin/activate
-        vulture MakerMatrix/ --config vulture.toml --sort-by-size > vulture_report.txt || true
+        vulture MakerMatrix/ --config pyproject.toml --sort-by-size > vulture_report.txt || true
         cat vulture_report.txt
 
     - name: Check for critical dead code
       run: |
         source venv_test/bin/activate
         # Fail if vulture finds high-confidence (>95%) unused code outside of tests
-        if vulture MakerMatrix/ --config vulture.toml --min-confidence 95 --exclude MakerMatrix/tests/ | grep -q "unused"; then
+        if vulture MakerMatrix/ --config pyproject.toml --min-confidence 95 --exclude MakerMatrix/tests/ | grep -q "unused"; then
           echo "❌ High-confidence dead code found!"
-          vulture MakerMatrix/ --config vulture.toml --min-confidence 95 --exclude MakerMatrix/tests/
+          vulture MakerMatrix/ --config pyproject.toml --min-confidence 95 --exclude MakerMatrix/tests/
           exit 1
         else
           echo "✅ No critical dead code found"

.env.https

@@ -1,11 +1,6 @@
-# Documentation files (except root README.md and CLAUDE.md)
-*.md
-**/*.md
-!/README.md
-!/CLAUDE.md
-
 # Claude Code configuration (user-specific)
 .claude/
+CLAUDE.md
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -266,3 +261,19 @@ MakerMatrix/backups/
 *.zip
 .env
 venv_ci_test/
+
+# Debug and test scripts (not part of the test suite)
+scripts/debug_*
+scripts/test_*
+scripts/verify_*
+test_output.txt
+
+# Security certificates and keystores
+*.pfx
+
+# Data and storage directories (generated at runtime)
+data/
+secure_storage/
+
+# Windows artifacts
+nul