feat(workflows): grant codebase-memory MCP tools to code-intel stages

Explicit per-stage grants (least-privilege, invariant #5) for the mounted
codebase-memory MCP side-car:
- role_pipeline: discovery bootstraps the graph (index_repository) + grounds;
  analyst/architect/decomposer/implementer/reviewer get read-only query tools
  (search_code/search_graph/get_architecture/trace_path/get_code_snippet)
  scoped to each role. NOTE: architect flips from pure-reasoning to tool-calling.
- review_loop implement+review and task_planning planner get read-only queries.

Tools are approval-gated at T2 (server default in config.toml [[mcp]]).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

examples/workflows/review_loop.toml

@@ -20,7 +20,12 @@ start = "implement"
 id = "implement"
 prompt = "prompts/implement.md"
 produces = [{ name = "patch", kind = "file_written" }]
-allowed_tools = ["file_write", "task_create", "task_update", "task_context", "task_search"]
+allowed_tools = [
+    "file_write", "task_create", "task_update", "task_context", "task_search",
+    "mcp__codebase-memory__search_code",
+    "mcp__codebase-memory__get_code_snippet",
+    "mcp__codebase-memory__trace_path",
+]
 token_budget = 8192
 max_retries = 3
 
@@ -31,7 +36,11 @@ id = "review"
 prompt = "prompts/review.md"
 needs = ["patch"]
 produces = [{ name = "review_report", kind = "review_report" }]
-allowed_tools = ["task_context", "task_update"]
+allowed_tools = [
+    "task_context", "task_update",
+    "mcp__codebase-memory__search_code",
+    "mcp__codebase-memory__trace_path",
+]
 token_budget = 8192
 max_retries = 3
 

examples/workflows/role_pipeline.toml

@@ -38,7 +38,15 @@ start = "discovery"
 id = "discovery"
 prompt = "prompts/discovery.md"
 produces = [{ name = "discovery", kind = "discovery" }]
-allowed_tools = ["file_read", "list_dir", "shell"]
+# Bootstraps the code-intelligence graph (index_repository) so downstream stages can query it,
+# plus grounds vetting against the real architecture. mcp__codebase-memory__* come from the
+# [[mcp]] side-car in config.toml.
+allowed_tools = [
+    "file_read", "list_dir", "shell",
+    "mcp__codebase-memory__index_repository",
+    "mcp__codebase-memory__search_code",
+    "mcp__codebase-memory__get_architecture",
+]
 token_budget = 16384
 max_retries = 2
 
@@ -49,7 +57,14 @@ max_retries = 2
 id = "analyst"
 prompt = "prompts/analyst.md"
 produces = [{ name = "analysis", kind = "analysis" }]
-allowed_tools = ["file_read", "shell", "task_search", "task_context", "task_create"]
+allowed_tools = [
+    "file_read", "shell", "task_search", "task_context", "task_create",
+    "mcp__codebase-memory__search_code",
+    "mcp__codebase-memory__search_graph",
+    "mcp__codebase-memory__get_architecture",
+    "mcp__codebase-memory__trace_path",
+    "mcp__codebase-memory__get_code_snippet",
+]
 ground_references = true
 token_budget = 16384
 max_retries = 2
@@ -60,6 +75,13 @@ id = "architect"
 prompt = "prompts/architect.md"
 needs = ["analysis"]
 produces = [{ name = "design", kind = "design" }]
+# Read-only code intelligence to decide component boundaries against the real call graph.
+# NOTE: this flips the architect from a pure-reasoning stage into a tool-calling one.
+allowed_tools = [
+    "mcp__codebase-memory__get_architecture",
+    "mcp__codebase-memory__search_graph",
+    "mcp__codebase-memory__trace_path",
+]
 token_budget = 16384
 max_retries = 2
 
@@ -71,7 +93,11 @@ max_retries = 2
 id = "decomposer"
 prompt = "prompts/task_planner.md"
 needs = ["design"]
-allowed_tools = ["file_read", "shell", "task_search", "task_context", "task_decompose", "task_create"]
+allowed_tools = [
+    "file_read", "shell", "task_search", "task_context", "task_decompose", "task_create",
+    "mcp__codebase-memory__search_code",
+    "mcp__codebase-memory__search_graph",
+]
 require_task_decompose = true
 token_budget = 16384
 max_retries = 2
@@ -88,6 +114,9 @@ claim_task = true
 allowed_tools = [
     "file_read", "file_write", "file_edit", "shell", "propose_scope",
     "task_create", "task_update", "task_context", "task_search",
+    "mcp__codebase-memory__search_code",
+    "mcp__codebase-memory__get_code_snippet",
+    "mcp__codebase-memory__trace_path",
 ]
 token_budget = 32768
 max_retries = 3
@@ -100,7 +129,12 @@ id = "reviewer"
 prompt = "prompts/reviewer.md"
 needs = ["patch", "analysis"]
 produces = [{ name = "review_report", kind = "review_report" }]
-allowed_tools = ["task_context", "task_update"]
+allowed_tools = [
+    "task_context", "task_update",
+    "mcp__codebase-memory__search_code",
+    "mcp__codebase-memory__trace_path",
+    "mcp__codebase-memory__get_code_snippet",
+]
 token_budget = 32768
 max_retries = 2
 

examples/workflows/task_planning.toml

@@ -9,7 +9,11 @@ start = "planner"
 [[stages]]
 id = "planner"
 prompt = "prompts/task_planner.md"
-allowed_tools = ["file_read", "shell", "task_search", "task_context", "task_decompose", "task_create"]
+allowed_tools = [
+    "file_read", "shell", "task_search", "task_context", "task_decompose", "task_create",
+    "mcp__codebase-memory__search_code",
+    "mcp__codebase-memory__search_graph",
+]
 require_task_decompose = true
 token_budget = 16384
 max_retries = 2