feat: Consolidate scripts folder (#183)

## Summary

Consolidates scattered scripts into a unified, organized structure as
specified in
[#173-consolidate-scripts-folder.md](./spec/173-consolidate-scripts-folder.md).

### Changes Made

- **Moved `bin/*` scripts to `./scripts`**: Unified all executable
scripts under single directory
- **Renamed `scripts/test` → `scripts/tests`**: Consistent with rest of
project naming conventions
- **Updated all references**: Fixed paths in Makefiles, documentation,
and test files
- **Fixed broken test paths**: Scripts tests now work with consolidated
structure

### Files Consolidation

**Before:**
```
bin/
├── check-dev.sh
├── common.sh  
├── mcp-test.py
├── release.sh
├── test-prereqs.sh
└── version.sh

scripts/
├── coverage_analysis.py
├── generate_canonical_tools.py
├── test/
└── version-utils.py
```

**After:**
```
scripts/
├── check-dev.sh
├── common.sh
├── coverage_analysis.py  
├── generate_canonical_tools.py
├── mcp-test.py
├── release.sh
├── test-prereqs.sh
├── tests/    # ← renamed from 'test'
├── version.sh
└── version-utils.py
```

### Test Results

- ✅ `make python-dist` - Works with updated script references
- ✅ `make test-scripts` - Finds tests in new `scripts/tests/` location  
- ✅ Script path tests fixed - No more `FileNotFoundError` for release.sh

### Benefits

1. **Improved discoverability** - All scripts in one logical location
2. **Consistent organization** - Matches project conventions (`tests/`
not `test/`)
3. **Reduced confusion** - No more wondering whether to check `bin/` or
`scripts/`
4. **Better maintainability** - Single location for script updates

🤖 Generated with [Claude Code](https://claude.ai/code)

---------

Co-authored-by: Claude <[email protected]>

Author: drernie

AGENTS.md

@@ -407,8 +407,8 @@ The following permissions are granted for this repository:
 - Workflow orchestration APIs reject blank workflow IDs; trim identifiers in tests when constructing fixtures to avoid silent acceptance.
 
 ### 2025-09-20 uv packaging notes
-- DXT packaging currently runs through `make.deploy` using `uv pip install`; the UV PyPI build flow lives in `bin/release.sh python-dist` with `make python-dist`, mirroring how `make dxt` exposes DXT packaging.
-- `python-dist` builds local artifacts without credentials. `bin/release.sh python-publish` (via `make python-publish`) requires either `UV_PUBLISH_TOKEN` or `UV_PUBLISH_USERNAME`/`UV_PUBLISH_PASSWORD`, defaults to TestPyPI (`PYPI_PUBLISH_URL`/`PYPI_REPOSITORY_URL` override), and respects `DIST_DIR`.
+- DXT packaging currently runs through `make.deploy` using `uv pip install`; the UV PyPI build flow lives in `scripts/release.sh python-dist` with `make python-dist`, mirroring how `make dxt` exposes DXT packaging.
+- `python-dist` builds local artifacts without credentials. `scripts/release.sh python-publish` (via `make python-publish`) requires either `UV_PUBLISH_TOKEN` or `UV_PUBLISH_USERNAME`/`UV_PUBLISH_PASSWORD`, defaults to TestPyPI (`PYPI_PUBLISH_URL`/`PYPI_REPOSITORY_URL` override), and respects `DIST_DIR`.
 - GitHub Actions builds dist artifacts via `python-dist`, publishes them with `pypa/gh-action-pypi-publish`, then runs `make dxt`, `make dxt-validate`, and `make release-zip` to keep DXT parity. Secrets supply the PyPI/TestPyPI token (`secrets.PYPI_TOKEN`).
 
 ## important-instruction-reminders

Makefile

@@ -95,13 +95,13 @@ config-claude:
 
 # Version Management Targets
 bump-patch:
-	@bin/release.sh bump patch
+	@scripts/release.sh bump patch
 
 bump-minor:
-	@bin/release.sh bump minor
+	@scripts/release.sh bump minor
 
 bump-major:
-	@bin/release.sh bump major
+	@scripts/release.sh bump major
 
 # Combined Release Targets (bump + commit + tag)
 release-patch: bump-patch
@@ -111,7 +111,7 @@ release-patch: bump-patch
 	git commit -m "bump: patch version to $$VERSION"; \
 	echo "✅ Committed version bump to $$VERSION"
 	@echo "🏷️  Creating release tag..."
-	@bin/release.sh release
+	@scripts/release.sh release
 
 release-minor: bump-minor
 	@echo "🔍 Committing minor version bump..."
@@ -120,7 +120,7 @@ release-minor: bump-minor
 	git commit -m "bump: minor version to $$VERSION"; \
 	echo "✅ Committed version bump to $$VERSION"
 	@echo "🏷️  Creating release tag..."
-	@bin/release.sh release
+	@scripts/release.sh release
 
 release-major: bump-major
 	@echo "🔍 Committing major version bump..."
@@ -129,4 +129,4 @@ release-major: bump-major
 	git commit -m "bump: major version to $$VERSION"; \
 	echo "✅ Committed version bump to $$VERSION"
 	@echo "🏷️  Creating release tag..."
-	@bin/release.sh release
+	@scripts/release.sh release

README.md

@@ -45,7 +45,7 @@ SERVER_PID=$!
 
 # 4. Verify that it works
 sleep 8
-bin/mcp-test.py http://127.0.0.1:8000/mcp/
+scripts/mcp-test.py http://127.0.0.1:8000/mcp/
 kill $SERVER_PID
 ```
 

bin/version.sh

@@ -11,7 +11,7 @@ DIST_DIR := dist
 # Variables
 DXT_NAME := quilt-mcp
 # Allow VERSION to be overridden from command line, otherwise read from pyproject.toml
-MANIFEST_VERSION := $(shell python3 scripts/version-utils.py get-version 2>/dev/null || echo "dev")
+MANIFEST_VERSION := $(shell python3 scripts/version.py get-version 2>/dev/null || echo "dev")
 PACKAGE_VERSION := $(if $(VERSION),$(VERSION),$(MANIFEST_VERSION))
 PACKAGE_ID := $(DIST_DIR)/$(DXT_NAME)-$(PACKAGE_VERSION)
 DXT_PACKAGE := $(PACKAGE_ID).dxt
@@ -47,7 +47,6 @@ $(ASSETS_MARKER): $(ASSET_FILES)
 	@mkdir -p $(BUILD_DIR)
 	@cp -r $(ASSETS_DIR)/* $(BUILD_DIR)/
 	@if [ -f "$(BUILD_DIR)/check-dxt.sh" ]; then chmod +x $(BUILD_DIR)/check-dxt.sh; fi
-	@if [ -f "$(BUILD_DIR)/check-prereqs.sh" ]; then chmod +x $(BUILD_DIR)/check-prereqs.sh; fi
 	@echo "Generating manifest.json from template..."
 	@sed 's/{{ version }}/$(PACKAGE_VERSION)/g' $(BUILD_DIR)/manifest.json.j2 > $(BUILD_DIR)/manifest.json
 	@rm $(BUILD_DIR)/manifest.json.j2
@@ -96,7 +95,7 @@ python-dist: check-tools
 	@echo "✅ Python packaging complete"
 
 python-publish:
-	@./bin/release.sh python-publish
+	@./scripts/release.sh python-publish
 
 # DXT Package Validation
 dxt-validate: check-tools dxt
@@ -126,18 +125,18 @@ release-tag:
 	@echo "Creating release tag..."
 	@if [ "${DRY_RUN}" = "1" ]; then \
 		echo "🔍 DRY RUN: Would create release tag"; \
-		./bin/release.sh release --dry-run; \
+		./scripts/release.sh release --dry-run; \
 	else \
-		./bin/release.sh release; \
+		./scripts/release.sh release; \
 	fi
 
 release-dev-tag:
 	@echo "Creating development tag..."
 	@if [ "${DRY_RUN}" = "1" ]; then \
 		echo "🔍 DRY RUN: Would create development tag"; \
-		./bin/release.sh dev --dry-run; \
+		./scripts/release.sh dev --dry-run; \
 	else \
-		./bin/release.sh dev; \
+		./scripts/release.sh dev; \
 	fi
 
 # Cleanup Targets

extract_tools.py

@@ -79,11 +79,11 @@ coverage-html:
 	@echo "✅ HTML coverage report generated in htmlcov/"
 	@echo "📊 Open htmlcov/index.html in your browser to view the report"
 
-test-scripts: scripts/test/test_*.py | $(RESULTS_DIR)
+test-scripts: scripts/tests/test_*.py | $(RESULTS_DIR)
 	@echo "Running script tests (coverage analysis, workflow behavior)..."
 	@uv sync --group test
-	@if [ -d "scripts/test" ] && [ "$$(find scripts/test -name "*.py" | wc -l)" -gt 0 ]; then \
-		export PYTHONPATH="src" && uv run python -m pytest scripts/test/ -v; \
+	@if [ -d "scripts/tests" ] && [ "$$(find scripts/tests -name "*.py" | wc -l)" -gt 0 ]; then \
+		export PYTHONPATH="src" && uv run python -m pytest scripts/tests/ -v; \
 	else \
 		echo "No script tests found"; \
 	fi