docs(readme): update script paths and remove Makefile references

Changes:
- Updated all script references to use scripts/ prefix
- Updated vendor repository count from 32+ to 40+
- Removed Makefile targets section (Makefile no longer primary interface)

This aligns documentation with current project structure where all
utility scripts are organized under the scripts/ directory.

README.md

@@ -64,74 +64,44 @@ For detailed build and configuration status of all MCP/LSP servers, see [STATUS.
 
 ### Setup Scripts
 
-The repository includes helpful scripts to simplify setup and management:
+The repository includes helpful scripts in the `scripts/` directory to simplify setup and management:
 
-#### CloneVendorRepos.sh
+#### scripts/CloneVendorRepos.sh
 Clone all upstream vendor MCP/LSP repositories:
 
 ```bash
-./CloneVendorRepos.sh
+./scripts/CloneVendorRepos.sh
 ```
 
-This script clones all 32+ vendor repositories into `vendor/` directory.
+This script clones all 40+ vendor repositories into `vendor/` directory.
 
-#### BuildAll.sh
+#### scripts/BuildAll.sh
 Build all MCP/LSP services:
 
 ```bash
-./BuildAll.sh
+./scripts/BuildAll.sh
 ```
 
 This script iterates through all services in `docker-compose.yml` and builds each one.
 
-#### CleanVendor.sh
+#### scripts/CleanVendor.sh
 Remove all cloned vendor repositories:
 
 ```bash
-./CleanVendor.sh
+./scripts/CleanVendor.sh
 ```
 
 ⚠️ **Warning**: This permanently deletes all cloned vendor repositories. You'll need to re-clone them.
 
-#### StatusCheck.sh
+#### scripts/StatusCheck.sh
 Check build status of all services:
 
 ```bash
-./StatusCheck.sh
+./scripts/StatusCheck.sh
 ```
 
 This script checks which Docker images exist and compares with `STATUS.md`.
 
-### Makefile Targets
-
-For a more command-line oriented approach, use the included Makefile:
-
-```bash
-# Show all available targets
-make help
-
-# Clone all vendor repositories
-make clone-vendors
-
-# Build all services
-make build-all
-
-# Clean vendor directory
-make clean-vendor
-
-# Check service status
-make status
-
-# Start all services
-make up
-
-# Stop all services
-make down
-
-# Rebuild specific service
-make rebuild SERVICE=context7-mcp
-```
-
 ## 💻 Usage
 
 ### Docker Compose Commands