Setup dev container and MCP infrastructure

Add dev container configuration with docker-compose, Dockerfile, and entrypoint script

- Create .devcontainer/devcontainer.json for VS Code dev container
- Create .devcontainer/docker-compose.yml for container setup
- Add Dockerfile with Python, Go, Rust, R, and jj tools
- Add docker-entrypoint.sh to initialize .ai_index and start mcp-server
- Add Makefile for container management and MCP operations
- Add .gitignore entries for AI index
- Add OpenCode global instructions
- Add basic MCP server and tool for listing Go imports
- Add Zed integration configuration
- Update README with project vision and structure

Makefile

@@ -0,0 +1,66 @@
+# Makefile pour dev container AI + MCP bootstrap
+
+# Variables
+PROJECT_DIR := $(shell pwd)
+CONTAINER_NAME := ai-dev-container
+WORKSPACE := /workspace
+MCP_LOG := $(WORKSPACE)/.ai_index/mcp.log
+
+# --- Dev Container Management ---
+
+# Build the container
+build:
+	docker build -t $(CONTAINER_NAME) .
+
+# Run interactive container with mounted project
+run:
+	docker run -v $(PROJECT_DIR):$(WORKSPACE) -it --rm $(CONTAINER_NAME)
+
+# Run container with MCP server in background
+run-mcp:
+	docker run -v $(PROJECT_DIR):$(WORKSPACE) -it --rm $(CONTAINER_NAME) bash
+
+# --- MCP / Index Management ---
+
+# Initialize .ai_index
+init-index:
+	@echo "[MAKE] Initializing .ai_index..."
+	mkdir -p $(PROJECT_DIR)/.ai_index/ast
+	mkdir -p $(PROJECT_DIR)/.ai_index/embeddings
+	@if [ ! -f $(PROJECT_DIR)/.ai_index/graph.db ]; then \
+		sqlite3 $(PROJECT_DIR)/.ai_index/graph.db "VACUUM;"; \
+	fi
+
+# Run MCP tool (list imports)
+mcp-list:
+	@echo "[MAKE] Running MCP list_imports.py..."
+	python3 $(PROJECT_DIR)/opt/dev-tools/list_imports.py --project $(WORKSPACE)
+
+# Update embeddings (example)
+embeddings:
+	@echo "[MAKE] Generating embeddings..."
+	python3 $(PROJECT_DIR)/opt/dev-tools/generate_embeddings.py --project $(WORKSPACE)
+
+# Update graph (example)
+update-graph:
+	@echo "[MAKE] Updating dependency graph..."
+	python3 $(PROJECT_DIR)/opt/dev-tools/update_graph.py --project $(WORKSPACE)
+
+# Clean logs and temporary files
+clean:
+	@echo "[MAKE] Cleaning .ai_index..."
+	rm -f $(PROJECT_DIR)/.ai_index/*.log
+	rm -rf $(PROJECT_DIR)/.ai_index/ast/*
+	rm -rf $(PROJECT_DIR)/.ai_index/embeddings/*
+
+# Restart MCP server inside container
+restart-mcp:
+	docker exec -it $(CONTAINER_NAME) bash -c "\
+		pkill -f mcp-server; \
+		/opt/bin/mcp-server --project $(WORKSPACE) > $(MCP_LOG) 2>&1 & \
+	"
+
+# --- Bootstrap for new project ---
+# Build container, init index
+bootstrap: build init-index
+	@echo "[MAKE] Bootstrap complete. Run 'make run' to start the container."