feat: Comprehensive Amplifier improvements with self-healing, Aider, and caching

.claude/commands/automation/aider.md

@@ -0,0 +1,16 @@
+---
+description: Launch Aider with Amplifier presets for targeted regeneration
+argument-hint: [files ...] [--options]
+allowed-tools: Bash
+---
+
+Start an Aider session using the Amplifier CLI wrapper. Arguments are passed directly to the CLI.
+
+Execute: !`python -m amplifier.cli aider $ARGUMENTS 2>&1`
+
+Use this command to open Aider against specific files or with additional flags (for example, `--zen` or `-m "refactor this"`).
+
+Examples:
+- `/aider mymodule.py --zen -m "Simplify this module"`
+- `/aider --mode chat -m "How should I structure this feature?"`
+- `/aider file1.py file2.py -m "Add error handling"`

.claude/commands/automation/heal.md

@@ -0,0 +1,17 @@
+---
+description: Run the Amplifier auto-healing workflow through the CLI
+argument-hint: [--check-only] [--max N] [--threshold SCORE]
+allowed-tools: Bash
+---
+
+Automate healing of unhealthy modules using the Amplifier CLI.
+
+## Current Status
+!`python -m amplifier.cli heal --check-only 2>&1`
+
+## Task
+Based on the health analysis above, run the healing process with the provided arguments (or use defaults if no arguments provided).
+
+Execute: !`python -m amplifier.cli heal --yes $ARGUMENTS 2>&1`
+
+Review the reported results and summarize the improvements made to each module.

.claude/settings.json

@@ -14,7 +14,7 @@
       ".vscode",
       ".claude",
       ".ai",
-      "~/amplifier"
+      "~/dev/amplifier"
     ]
   },
   "enableAllProjectMcpServers": false,

.gitignore

@@ -1,62 +1,77 @@
-# Private settings
-**/certs/*.pem
-**/certs/config.json
-**/certs/mkcert
-.env
-*.local
-*.user
-*__local__*
-appsettings.*.json
-**/.DS_Store
-
-# Dependencies and build cache
-node_modules
-.venv
-__pycache__
-.pytest_cache
-.ruff_cache
-.cache
-*.egg-info
-bin
-obj
-dist
-build
-
-# Logs
-*.log
-npm-debug.log*
-yarn-debug.log*
-yarn-error.log*
-pnpm-debug.log*
-lerna-debug.log*
-
-#azd files
-.azure
-azure.yaml
-next-steps.md
-
-# Generated files
-output
-logs
-
-# Test files
-.coverage
-
-# Working folders
-ai_working/tmp
-.tmp
-
-# Ignore Windows Alternate Data Streams (ADS) files that may appear in WSL
-**/*Zone.Identifier
-**/*:Zone.Identifier
-**/*sec.endpointdlp
-**/*:sec.endpointdlp
-
-# Default data directory
-.data/
-
-# .claude-trace Logs
-.claude-trace
-
-# Smoke test runtime logs
-.smoke_test_data/data
+# Private settings
+**/certs/*.pem
+**/certs/config.json
+**/certs/mkcert
+.env
+*.local
+*.user
+*__local__*
+appsettings.*.json
+**/.DS_Store
+
+# Dependencies and build cache
+node_modules
+.venv
+__pycache__
+.pytest_cache
+.ruff_cache
+.cache
+*.egg-info
+# bin directory for build artifacts (but allow our global command)
+# bin
+obj
+dist
+build
+
+# Logs
+*.log
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+pnpm-debug.log*
+lerna-debug.log*
+
+#azd files
+.azure
+azure.yaml
+next-steps.md
+
+# Generated files
+output
+logs
+
+# Test files
+.coverage
+
+# Working folders
+ai_working/tmp
+.tmp
+
+# Ignore Windows Alternate Data Streams (ADS) files that may appear in WSL
+**/*Zone.Identifier
+**/*:Zone.Identifier
+**/*sec.endpointdlp
+**/*:sec.endpointdlp
+
+# Default data directory
+.data/
+
+# .claude-trace Logs
+.claude-trace
+
+# Smoke test runtime logs
+.smoke_test_data/data
+
+# Aider artifacts
+.aider*
+.aider.*/
+
+# Test reports and temporary test files
+*_TEST_REPORT.md
+test_pr*.py
+test_cli_*.py
+
+# Temporary files that might be accidentally created
+evaluate
+repo
+this

AIDER_PR.md

@@ -0,0 +1,44 @@
+# Add Aider Tools for AI-Powered Code Regeneration
+
+## Summary
+
+This PR adds standalone Aider tools to Amplifier, enabling AI-powered module regeneration using different development philosophies.
+
+## What's Included
+
+- **`amplifier/tools/aider_regenerator.py`**: Core regeneration tool with support for three philosophies (fractalized, modular, zen)
+- **`scripts/setup-aider.sh`**: Installation script for setting up Aider in an isolated environment
+- **`docs/aider-tools.md`**: Comprehensive documentation
+
+## Key Features
+
+- **Philosophy-based regeneration**: Choose between fractalized thinking, modular design, or zen simplicity
+- **Batch processing**: Regenerate multiple modules at once
+- **Specification support**: Regenerate based on explicit specifications
+- **Isolated installation**: Aider runs in its own virtual environment to avoid dependency conflicts
+
+## Usage
+
+```bash
+# Setup
+bash scripts/setup-aider.sh
+
+# Regenerate a module
+python amplifier/tools/aider_regenerator.py amplifier/my_module.py --philosophy zen
+```
+
+## Why This Matters
+
+AI-powered code regeneration allows for:
+- Consistent code quality improvements
+- Philosophy-aligned refactoring
+- Automated technical debt reduction
+- Faster iteration on module design
+
+## Testing
+
+The tool has been tested with:
+- Single module regeneration
+- Batch processing
+- Different philosophy modes
+- Error handling (missing files, timeout scenarios)

Makefile

@@ -21,6 +21,7 @@ default: ## Show essential commands
 	@echo ""
 	@echo "Quick Start:"
 	@echo "  make install         Install all dependencies"
+	@echo "  make install-global  Install global 'amplifier' command"
 	@echo ""
 	@echo "Knowledge Base:"
 	@echo "  make knowledge-update        Full pipeline: extract & synthesize"
@@ -54,6 +55,7 @@ help: ## Show ALL available commands
 	@echo ""
 	@echo "QUICK START:"
 	@echo "  make install         Install all dependencies"
+	@echo "  make install-global  Install global 'amplifier' command"
 	@echo ""
 	@echo "KNOWLEDGE BASE:"
 	@echo "  make knowledge-update        Full pipeline: extract & synthesize"
@@ -140,6 +142,9 @@ install: ## Install all dependencies
 	@echo ""
 	@echo "✅ All dependencies installed!"
 	@echo ""
+	@echo "💡 For global access to Amplifier from any directory:"
+	@echo "   make install-global"
+	@echo ""
 	@if [ -n "$$VIRTUAL_ENV" ]; then \
 		echo "✓ Virtual environment already active"; \
 	elif [ -f .venv/bin/activate ]; then \
@@ -148,6 +153,67 @@ install: ## Install all dependencies
 		echo "✗ No virtual environment found. Run 'make install' first."; \
 	fi
 
+# Global installation
+install-global: ## Install global 'amplifier' command for system-wide access
+	@echo "Installing global Amplifier command..."
+	@if [ ! -f .venv/bin/activate ]; then \
+		echo "❌ Please run 'make install' first to create the virtual environment"; \
+		exit 1; \
+	fi
+	@mkdir -p ~/bin
+	@cp bin/amplifier ~/bin/amplifier
+	@chmod +x ~/bin/amplifier
+	@echo "✅ Global 'amplifier' command installed to ~/bin/amplifier"
+	@echo ""
+	@if echo "$$PATH" | grep -q "$$HOME/bin"; then \
+		echo "✓ ~/bin is already in your PATH"; \
+	else \
+		echo "💡 Add ~/bin to your PATH for global access:"; \
+		if [ -n "$$ZSH_VERSION" ] || [ "$$SHELL" = "/bin/zsh" ] || [ -f ~/.zshrc ]; then \
+			echo '   echo "export PATH="\$$HOME/bin:\$$PATH"" >> ~/.zshrc'; \
+			echo "   source ~/.zshrc"; \
+		else \
+			echo '   echo "export PATH="\$$HOME/bin:\$$PATH"" >> ~/.bashrc'; \
+			echo "   source ~/.bashrc"; \
+		fi; \
+	fi
+	@echo ""
+	@echo "Usage: amplifier [project-dir] [claude-options]"
+	@echo "Example: amplifier ~/my-project --model sonnet"
+
+install-global-system: ## Install global 'amplifier' command system-wide (requires sudo)
+	@echo "Installing system-wide Amplifier command..."
+	@if [ ! -f .venv/bin/activate ]; then \
+		echo "❌ Please run 'make install' first to create the virtual environment"; \
+		exit 1; \
+	fi
+	@echo "This will install to /usr/local/bin and requires sudo privileges."
+	@read -p "Continue? [y/N] " -n 1 -r; echo; \
+	if [[ $$REPLY =~ ^[Yy]$$ ]]; then \
+		sudo cp bin/amplifier /usr/local/bin/amplifier; \
+		sudo chmod +x /usr/local/bin/amplifier; \
+		echo "✅ Global 'amplifier' command installed to /usr/local/bin/amplifier"; \
+	else \
+		echo "Installation cancelled."; \
+	fi
+
+uninstall-global: ## Remove global 'amplifier' command
+	@echo "Removing global Amplifier command..."
+	@if [ -f ~/bin/amplifier ]; then \
+		rm ~/bin/amplifier; \
+		echo "✅ Removed ~/bin/amplifier"; \
+	else \
+		echo "✓ ~/bin/amplifier not found"; \
+	fi
+	@if [ -f /usr/local/bin/amplifier ]; then \
+		echo "System-wide installation found at /usr/local/bin/amplifier"; \
+		read -p "Remove it? (requires sudo) [y/N] " -n 1 -r; echo; \
+		if [[ $$REPLY =~ ^[Yy]$$ ]]; then \
+			sudo rm /usr/local/bin/amplifier; \
+			echo "✅ Removed /usr/local/bin/amplifier"; \
+		fi; \
+	fi
+
 # Code quality
 check: ## Format, lint, and type-check all code
 	@# Handle worktree virtual environment issues by unsetting mismatched VIRTUAL_ENV