Remove internal phase comments and format code

Strip all Phase references, TODO/FUTURE roadmap notes, and internal
planning comments from the codebase. Run Prettier for consistent
formatting across all Java files.

Makefile

@@ -138,6 +138,16 @@ idea: ## Generate IntelliJ IDEA run configurations
 eclipse: ## Generate Eclipse project files
 	@$(GRADLE) eclipse
 
+##@ Formatting
+
+.PHONY: format
+format: ## Format code using Prettier
+	@npx --yes prettier --plugin prettier-plugin-java --tab-width 4 --write "src/**/*.java"
+
+.PHONY: check-format
+check-format: ## Check code formatting
+	@npx --yes prettier --plugin prettier-plugin-java --tab-width 4 --check "src/**/*.java"
+
 ##@ Information
 
 .PHONY: info