170 tool audit (#177)

- **rename script**
- **trim spec**
- **phases**
- **phase 1**
- **package_contents_search**
- **feat: consolidate catalog search tooling**

---------

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
 ```
 
@@ -142,25 +142,25 @@ This server provides **84+ comprehensive tools** organized into categories:
 
 - `packages_list` - List packages with filtering and search
 - `package_browse` - Explore package contents and structure  
-- `package_create` - Create packages from S3 objects
+- `package_create` - Create packages with metadata templates and validation
 - `package_update` - Update existing packages
 - `package_validate` - Validate package integrity
-- `create_package_enhanced` - Advanced creation with templates
+- `package_tools_list` - Discover all package management helpers
 
 ### 🗄️ S3 Operations  
 
 - `bucket_objects_list` - List and filter S3 objects
 - `bucket_object_info` - Get detailed object metadata
 - `bucket_object_text` - Read text content from objects
 - `bucket_objects_put` - Upload multiple objects
-- `bucket_objects_search` - Search using Elasticsearch
+
 
 ### 📊 Analytics & SQL
 
 - `athena_query_execute` - Run SQL queries via Athena
 - `athena_databases_list` - List available databases
 - `tabulator_tables_list` - Manage Quilt Tabulator tables
-- `unified_search` - Multi-backend intelligent search
+- `catalog_search` - Multi-backend intelligent search
 
 ### 🔐 Authentication & Permissions
 
@@ -173,7 +173,6 @@ This server provides **84+ comprehensive tools** organized into categories:
 - `workflow_create` - Multi-step workflow management
 - `metadata_templates` - Generate metadata (genomics, ML, etc.)
 - `generate_quilt_summarize_json` - Create package summaries
-- `create_package_from_s3` - Smart S3-to-package conversion
 
 **[View complete tool reference →](docs/TOOLS.md)**
 
@@ -379,7 +378,7 @@ await mcp_client.call_tool(\"unified_search\", {
 })
 
 # Create package
-await mcp_client.call_tool(\"create_package_enhanced\", {
+await mcp_client.call_tool(\"package_create\", {
     \"name\": \"genomics/study-001\",
     \"files\": [\"s3://bucket/data.vcf\"],
     \"metadata_template\": \"genomics\",

bin/version.sh

@@ -1109,12 +1109,12 @@ result = await mcp_client.call_tool(\"workflow_create\", {
 }
 ```
 
-#### `workflow_add_step`
+#### `workflow_step_add`
 
 Add steps to existing workflows.
 
 ```python
-result = await mcp_client.call_tool(\"workflow_add_step\", {
+result = await mcp_client.call_tool(\"workflow_step_add\", {
     \"workflow_id\": \"genomics-processing-001\",
     \"step_id\": \"quality_control\",
     \"description\": \"Run FastQC on raw sequencing data\",
@@ -1127,7 +1127,7 @@ result = await mcp_client.call_tool(\"workflow_add_step\", {
 })
 
 # Add dependent step
-result = await mcp_client.call_tool(\"workflow_add_step\", {
+result = await mcp_client.call_tool(\"workflow_step_add\", {
     \"workflow_id\": \"genomics-processing-001\",
     \"step_id\": \"alignment\",
     \"description\": \"Align reads to reference genome\",
@@ -1140,12 +1140,12 @@ result = await mcp_client.call_tool(\"workflow_add_step\", {
 })
 ```
 
-#### `workflow_update_step`
+#### `workflow_step_update`
 
 Update step status and results.
 
 ```python
-result = await mcp_client.call_tool(\"workflow_update_step\", {
+result = await mcp_client.call_tool(\"workflow_step_update\", {
     \"workflow_id\": \"genomics-processing-001\",
     \"step_id\": \"quality_control\",
     \"status\": \"completed\",
@@ -1157,12 +1157,12 @@ result = await mcp_client.call_tool(\"workflow_update_step\", {
 })
 ```
 
-#### `workflow_get_status`
+#### `workflow_status_get`
 
 Get comprehensive workflow status.
 
 ```python
-result = await mcp_client.call_tool(\"workflow_get_status\", {
+result = await mcp_client.call_tool(\"workflow_status_get\", {
     \"workflow_id\": \"genomics-processing-001\"
 })
 
@@ -1189,12 +1189,12 @@ result = await mcp_client.call_tool(\"workflow_get_status\", {
 }
 ```
 
-#### `workflow_list_all`
+#### `workflow_list`
 
 List all workflows with summary information.
 
 ```python
-result = await mcp_client.call_tool(\"workflow_list_all\", {})
+result = await mcp_client.call_tool(\"workflow_list\", {})
 
 # Response includes workflow summaries
 {
@@ -1273,13 +1273,13 @@ result = await mcp_client.call_tool(\"list_metadata_templates\", {})
 }
 ```
 
-#### `get_metadata_template`
+#### `metadata_template_get`
 
 Get a specific metadata template with optional custom fields.
 
 ```python
 # Get genomics template
-result = await mcp_client.call_tool(\"get_metadata_template\", {
+result = await mcp_client.call_tool(\"metadata_template_get\", {
     \"template_name\": \"genomics\",
     \"custom_fields\": {
         \"study_id\": \"CCLE_2024\",
@@ -1306,12 +1306,12 @@ result = await mcp_client.call_tool(\"get_metadata_template\", {
 }
 ```
 
-#### `create_metadata_from_template`
+#### `metadata_template_create`
 
 Create metadata using a template - simplified interface.
 
 ```python
-result = await mcp_client.call_tool(\"create_metadata_from_template\", {
+result = await mcp_client.call_tool(\"metadata_template_create\", {
     \"template_name\": \"genomics\",
     \"description\": \"Human RNA-seq data from CCLE cell lines\",
     \"custom_fields\": {
@@ -2046,22 +2046,22 @@ workflow = await mcp_client.call_tool(\"workflow_create\", {
 })
 
 # Add processing steps
-qc_step = await mcp_client.call_tool(\"workflow_add_step\", {
+qc_step = await mcp_client.call_tool(\"workflow_step_add\", {
     \"workflow_id\": \"data-processing-pipeline\",
     \"step_id\": \"quality_control\",
     \"description\": \"Quality control analysis\",
     \"step_type\": \"automated\"
 })
 
-alignment_step = await mcp_client.call_tool(\"workflow_add_step\", {
+alignment_step = await mcp_client.call_tool(\"workflow_step_add\", {
     \"workflow_id\": \"data-processing-pipeline\",
     \"step_id\": \"alignment\",
     \"description\": \"Read alignment to reference\",
     \"dependencies\": [\"quality_control\"]
 })
 
 # Monitor workflow progress
-status = await mcp_client.call_tool(\"workflow_get_status\", {
+status = await mcp_client.call_tool(\"workflow_status_get\", {
     \"workflow_id\": \"data-processing-pipeline\"
 })
 ```
@@ -2075,8 +2075,8 @@ status = await mcp_client.call_tool(\"workflow_get_status\", {
 | **S3 Operations** | `bucket_objects_list`, `bucket_object_info`, `unified_search` | Direct data access, file operations |
 | **Search & Discovery** | `unified_search`, `search_suggest`, `packages_search` | Finding data, content discovery |
 | **Analytics** | `athena_query_execute`, `tabulator_tables_list` | Data analysis, SQL queries |
-| **Workflows** | `workflow_create`, `workflow_add_step`, `workflow_get_status` | Process orchestration, automation |
-| **Metadata** | `get_metadata_template`, `validate_metadata_structure` | Data documentation, standardization |
+| **Workflows** | `workflow_create`, `workflow_step_add`, `workflow_status_get` | Process orchestration, automation |
+| **Metadata** | `metadata_template_get`, `validate_metadata_structure` | Data documentation, standardization |
 | **Permissions** | `aws_permissions_discover`, `bucket_access_check` | Security, access validation |
 | **Administration** | `admin_users_list`, `admin_user_create`, `admin_roles_list` | User management, role management |
 

docs/api/TOOLS.md

@@ -118,7 +118,7 @@ This document describes the implementation of a dual MCP (Model Context Protocol
 **Workflow**:
 1. `benchling_search_entities` - Validate Library L-789 exists
 2. `mcp_quilt_package_create_from_s3` - Create Quilt package from FASTQ files
-3. `mcp_quilt_create_metadata_from_template` - Add Benchling entity links to metadata
+3. `mcp_quilt_metadata_template_create` - Add Benchling entity links to metadata
 4. `benchling_get_projects` - Update project with package reference
 
 ### 3. Protocol Awareness (SB010)

docs/archive/DUAL_MCP_ARCHITECTURE.md

@@ -38,7 +38,7 @@ After running comprehensive testing against 40 realistic test cases, the MCP ser
 **Affected Tools**:
 - `mcp_quilt_package_validate`
 - `mcp_quilt_package_update_metadata`
-- `mcp_quilt_create_metadata_from_template`
+- `mcp_quilt_metadata_template_create`
 - `mcp_quilt_fix_metadata_validation_issues`
 - `mcp_quilt_show_metadata_examples`
 - `mcp_quilt_bucket_recommendations_get`

docs/archive/MCP_COMPREHENSIVE_ANALYSIS.md

@@ -45,7 +45,7 @@ After running actual user queries against the real MCP server, I've discovered s
 ---
 
 ### **R003: "Create a new package with metadata and validate the metadata structure"**
-**MCP Decision**: `get_metadata_template` + `validate_metadata_structure`
+**MCP Decision**: `metadata_template_get` + `validate_metadata_structure`
 **Actual Result**: ✅ **GOOD**
 - Retrieved genomics metadata template
 - Validated custom metadata structure successfully

docs/archive/REAL_MCP_QUERY_ANALYSIS.md

@@ -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