Refactor the project

Author: habedi

.gitignore

@@ -166,3 +166,5 @@ BINHARIC.md
 AGENT.md
 *.tar.gz
 *.tgz
+test.txt
+a.out

Makefile

@@ -37,34 +37,34 @@ help: ## Show this help message
 	awk 'BEGIN {FS = ":.*?## "}; {printf "  \033[36m%-18s\033[0m %s\n", $$1, $$2}'
 
 install: ## Install project dependencies
-	$(PACKAGE_MANAGER) install --legacy-peer-deps
+	@$(PACKAGE_MANAGER) install --legacy-peer-deps
 
 build: check-deps ## Build Binharic
-	$(PACKAGE_MANAGER) run build
+	@$(PACKAGE_MANAGER) run build
 
 run: build ## Start Binharic in terminal
-	$(PACKAGE_MANAGER) start
+	@$(PACKAGE_MANAGER) start
 
 clean: ## Remove build artifacts
-	rm -rf dist $(NODE_MODULES_DIR) $(REMOVABLE_THINGS)
+	@rm -rf dist $(NODE_MODULES_DIR) $(REMOVABLE_THINGS)
 
 # ==============================================================================
 # DEVELOPMENT
 # ==============================================================================
 test: check-deps ## Run the test suite
-	$(PACKAGE_MANAGER) test
+	@$(PACKAGE_MANAGER) test
 
 coverage: check-deps ## Run the test suite and generate a coverage report
-	$(PACKAGE_MANAGER) run coverage
+	@$(PACKAGE_MANAGER) run coverage
 
 lint: check-deps ## Run linter checks
-	$(PACKAGE_MANAGER) run lint
+	@$(PACKAGE_MANAGER) run lint
 
 typecheck: check-deps ## Run TypeScript type checks
-	$(PACKAGE_MANAGER) run typecheck
+	@$(PACKAGE_MANAGER) run typecheck
 
 format: check-deps ## Format code with Prettier
-	$(PACKAGE_MANAGER) run format
+	@$(PACKAGE_MANAGER) run format
 
 # ==============================================================================
 # GIT HOOKS
@@ -87,28 +87,28 @@ test-hooks: ## Test Git hooks on all files
 # PUBLISHING
 # ==============================================================================
 npm-login: ## Log in to npm registry
-	$(PACKAGE_MANAGER) login
+	@$(PACKAGE_MANAGER) login
 
 npm-whoami: ## Show current npm user (if logged in)
-	-$(PACKAGE_MANAGER) whoami
+	@-$(PACKAGE_MANAGER) whoami
 
 pack: build ## Create npm tarball (binharic-cli-<version>.tgz)
-	$(PACKAGE_MANAGER) pack
+	@$(PACKAGE_MANAGER) pack
 
 pack-dry-run: build ## Preview files that would be packed
-	$(PACKAGE_MANAGER) pack --dry-run
+	@$(PACKAGE_MANAGER) pack --dry-run
 
 publish-dry-run: ## Simulate npm publish (no registry changes)
-	$(PACKAGE_MANAGER) publish --dry-run
+	@$(PACKAGE_MANAGER) publish --access public --dry-run
 
 publish: ## Publish the package to npm (runs build via prepublishOnly)
-	$(PACKAGE_MANAGER) publish
+	@$(PACKAGE_MANAGER) publish --access public
 
 version-patch: ## Bump patch version (x.y.z -> x.y.(z+1))
-	$(PACKAGE_MANAGER) version patch
+	@$(PACKAGE_MANAGER) version patch
 
 version-minor: ## Bump minor version (x.y.z -> x.(y+1).0)
-	$(PACKAGE_MANAGER) version minor
+	@$(PACKAGE_MANAGER) version minor
 
 version-major: ## Bump major version ((x+1).0.0)
-	$(PACKAGE_MANAGER) version major
+	@$(PACKAGE_MANAGER) version major

README.md

@@ -9,7 +9,7 @@
 [![Tests](https://img.shields.io/github/actions/workflow/status/CogitatorTech/binharic-cli/tests.yml?label=tests&style=flat&labelColor=333333&logo=github&logoColor=white)](https://github.com/CogitatorTech/binharic-cli/actions/workflows/tests.yml)
 [![Code Coverage](https://img.shields.io/codecov/c/github/CogitatorTech/binharic-cli?style=flat&label=coverage&labelColor=333333&logo=codecov&logoColor=white)](https://codecov.io/gh/CogitatorTech/binharic-cli)
 [![Code Quality](https://img.shields.io/codefactor/grade/github/CogitatorTech/binharic-cli?style=flat&label=code%20quality&labelColor=333333&logo=codefactor&logoColor=white)](https://www.codefactor.io/repository/github/CogitatorTech/binharic-cli)
-[![npm](https://img.shields.io/npm/v/binharic-cli?style=flat&labelColor=333333&logo=npm&logoColor=white)](https://www.npmjs.com/package/binharic-cli)
+[![npm](https://img.shields.io/npm/v/%40cogitator%2Fbinharic-cli?style=flat&labelColor=333333&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cogitator/binharic-cli)
 [![Documentation](https://img.shields.io/badge/docs-latest-8ca0d7?style=flat&labelColor=333333&logo=read-the-docs&logoColor=white)](docs)
 [![License](https://img.shields.io/badge/license-MIT-00acc1?style=flat&labelColor=333333&logo=open-source-initiative&logoColor=white)](LICENSE)
 

ROADMAP.md

@@ -28,7 +28,7 @@ It includes planned features, improvements, and their current implementation sta
     - [x] Transient error handling with exponential backoff
     - [x] Tool execution confirmation flow
     - [x] AI SDK 5 Agent class integration
-    - [x] Automatic loop control with stopWhen conditions**
+    - [x] Automatic loop control with stopWhen conditions\*\*
     - [x] Budget-based stopping conditions
     - [x] Error threshold conditions
     - [x] Validation-based stopping
@@ -103,7 +103,7 @@ It includes planned features, improvements, and their current implementation sta
     - [x] File search with @ mention
     - [x] Non-blocking UI during LLM responses
     - [x] Command syntax highlighting (partial match in yellow, full match in cyan)
-    - [x] Colored help menu items**
+    - [x] Colored help menu items\*\*
     - [x] Clean message display (no "Binharic:" prefix)
     - [x] Dynamic username from system (not hardcoded)
     - [x] Tool results hidden from UI (only failures shown)
@@ -242,7 +242,7 @@ It includes planned features, improvements, and their current implementation sta
     - [x] Multi-step tool execution with automatic loop control
     - [x] Specialized agents with distinct personalities
     - [x] onStepFinish callbacks for monitoring
-    - [x] prepareStep callbacks for dynamic configuration**
+    - [x] prepareStep callbacks for dynamic configuration\*\*
     - [x] Multiple stopping conditions (step count, budget, errors, validation, completion)
     - [ ] Goal-oriented planning
     - [ ] Task decomposition