diff --git a/README.md b/README.md
index cf8a45b62..5772a8b7b 100644
--- a/README.md
+++ b/README.md
@@ -186,7 +186,7 @@ Removes all agent configs, skills, hooks, and instructions. Does not remove the
 - **Single static binary, zero infrastructure**: SQLite-backed, persists to `~/.cache/codebase-memory-mcp/`
 - **Auto-sync**: Background watcher detects file changes and re-indexes automatically
 - **Route nodes**: REST endpoints are first-class graph entities
-- **CLI mode**: `codebase-memory-mcp cli search_graph '{"name_pattern": ".*Handler.*"}'`
+- **CLI mode**: `codebase-memory-mcp cli search_graph '{"project": "my-project", "name_pattern": ".*Handler.*"}'`
 - **Available on**: npm, PyPI, Homebrew, Scoop, Winget, Chocolatey, AUR, `go install`
 
 ## Team-Shared Graph Artifact
@@ -397,11 +397,13 @@ Every MCP tool can be invoked from the command line:
 
 ```bash
 codebase-memory-mcp cli index_repository '{"repo_path": "/path/to/repo"}'
-codebase-memory-mcp cli search_graph '{"name_pattern": ".*Handler.*", "label": "Function"}'
-codebase-memory-mcp cli trace_path '{"function_name": "Search", "direction": "both"}'
-codebase-memory-mcp cli query_graph '{"query": "MATCH (f:Function) RETURN f.name LIMIT 5"}'
 codebase-memory-mcp cli list_projects
-codebase-memory-mcp cli --raw search_graph '{"label": "Function"}' | jq '.results[].name'
+
+# Use the "name" returned by list_projects as the project value.
+codebase-memory-mcp cli search_graph '{"project": "my-project", "name_pattern": ".*Handler.*", "label": "Function"}'
+codebase-memory-mcp cli trace_path '{"project": "my-project", "function_name": "Search", "direction": "both"}'
+codebase-memory-mcp cli query_graph '{"project": "my-project", "query": "MATCH (f:Function) RETURN f.name LIMIT 5"}'
+codebase-memory-mcp cli --raw search_graph '{"project": "my-project", "label": "Function"}' | jq '.results[].name'
 ```
 
 ## MCP Tools