analyze-codebase

name	analyze-codebase
description	Deep structural analysis of codebase using communities, flows, wiki, and embedding search. Understand architecture, execution paths, and module boundaries without reading files.
argument-hint	[module name, feature area, or question]

Analyze Codebase

Use the knowledge graph for deep structural analysis — architecture, execution flows, community clustering, and cross-file relationships.

Step 1: Orient with Stats and Architecture

list_graph_stats_tool()              # files, nodes, edges, languages, last updated
get_architecture_overview_tool()     # community map + coupling warnings
get_architecture_skeleton(level="containers")   # C4 skeleton — module map in 20 lines
get_project_standards()                          # project conventions from prompts/

The architecture overview groups code into communities (clusters of tightly related code) and identifies cross-community coupling. High coupling between communities is a design smell.

The architecture skeleton (.code-review-graph/architecture.c4) provides a persistent Mermaid C4 view of the codebase — containers (from communities) and components (from nodes). Read it first for a quick module map. If it doesn't exist yet, run code-review-graph c4 to generate it.

Project standards (prompts/ directory) define cross-project conventions: architecture patterns, coding style, tech stack. Use get_project_standards() to list available sections, then get_project_standards(section="patterns") to read a specific one.

Step 2: Explore Communities

# exclude_tests=True is the DEFAULT for communities and architecture tools.
# Without it, ~40% of communities are test files and dominate the overview.
list_communities_tool(sort_by="size")                    # production communities (default)
list_communities_tool(sort_by="cohesion")                # tightest clusters first
list_communities_tool(exclude_tests=False)               # include test communities too
get_community_tool(community_name="auth")                # details + member list
# If multiple communities share the name → status:"ambiguous" + matches:[{id,name}...]
# Use community_id= to select unambiguously

get_architecture_overview_tool()                         # production coupling map (default)
get_architecture_overview_tool(exclude_tests=False)      # show test communities in coupling too

Communities are detected automatically via the Leiden algorithm. Each community represents a logical module boundary — useful for understanding ownership and change impact.

Step 3: Find Code by Keyword or Structure

# Semantic / keyword search — multi-word query = FTS5 OR (one round-trip)
semantic_search_nodes_tool(query="authentication", kind="Function", limit=10)
semantic_search_nodes_tool(query="GraphStore",     kind="Class")
semantic_search_nodes_tool(query="migrations",     kind="File")

# exclude_tests=True is the DEFAULT — test helpers are filtered automatically.
# Pass exclude_tests=False only when you explicitly want test nodes in results.
semantic_search_nodes_tool(query="create_task")                          # production only (default)
semantic_search_nodes_tool(query="create_task", exclude_tests=False)     # include test helpers too

# Filter by language — useful in mixed-language repos (Python + TypeScript):
semantic_search_nodes_tool(query="build_graph", language="python")       # Python only

# Bulk multi-symbol lookup in one call:
semantic_search_nodes_tool(query="create_task add_task_edge move_task archive_task")

# Filter to a specific file:
semantic_search_nodes_tool(query="create", file_path="tasks.py")

# Returns: id, name, qualified_name, file_path, line_start, line_end, params, signature
# If single-token query matches 4+ nodes with the same name, response includes
# "disambiguation_note" suggesting to add file_path= to narrow results.

line_end is critical for large codebases. It tells you the exact boundary of a function without reading the file. Use it to do a targeted Read(offset=line_start, limit=line_end-line_start+1) only when you actually need the body — never read the whole file just to find where a function ends. Reading large functions bloats input context significantly while output context stays the same.

Use id or qualified_name from results directly in task_link_code(task_id, links=[{ref_type, code_node_id|qualified_name}]) or contract_add.

# File and pattern search
find_files_by_pattern_tool(patterns=["*router*", "src/**/*.ts", "main.*"])
find_large_functions_tool(min_lines=80, kind="Function")   # decomposition targets
find_large_functions_tool(min_lines=200, kind="File")      # oversized files

Step 4: Trace Relationships

query_graph_tool(pattern="callers_of",   target="create_task")                    # who calls this
query_graph_tool(pattern="callers_of",   target="create_task", exclude_tests=True) # production callers only
query_graph_tool(pattern="callers_of",   target="create_task", limit=20)           # cap large result sets
query_graph_tool(pattern="callees_of",   target="export_task")                    # what this calls
query_graph_tool(pattern="callees_of",   target="export_task", kind="Function")   # only Function callees
query_graph_tool(pattern="imports_of",   target="code_review_graph/tasks.py")
query_graph_tool(pattern="importers_of", target="code_review_graph/graph.py")
query_graph_tool(pattern="children_of",  target="code_review_graph/tasks.py")  # file contents
query_graph_tool(pattern="tests_for",    target="hybrid_search")     # test coverage
query_graph_tool(pattern="inheritors_of",target="GraphStore")        # subclasses
query_graph_tool(pattern="file_summary", target="code_review_graph/main.py")

All results include id and qualified_name for direct use in task/contract linking.

exclude_tests=True (default) filters test callers/importers. Popular functions can have 100+ test callers — always use limit=20 as a starting point and add exclude_tests=True to see only production call sites.

Step 5: Understand Execution Flows

list_flows_tool(is_test=False, language="python", sort_by="depth", limit=20)
# ↑ RECOMMENDED for /design-feature: surfaces real user-facing entry points (deep call chains)
# sort_by="criticality" ranks by number of callers — helper functions outrank MCP handlers.
# sort_by="depth" ranks by call chain length — actual entry points (CLI, MCP) have deepest paths.
list_flows_tool(sort_by="criticality", limit=20)            # most called functions (often helpers)
list_flows_tool(kind="Test")                                # test entry points only
# Without is_test=False, test functions dominate by criticality score.
# Without language="python", TypeScript VS Code extension flows may appear.

get_flow_tool(flow_name="handle_request")          # full call path with line numbers
get_flow_tool(flow_id=42, include_source=True)     # with source snippets

Flows show complete call chains from entry points (HTTP handlers, CLI commands, tests) through the codebase. Use criticality score to prioritize review effort.

Step 6: Generate and Browse Wiki

generate_wiki_tool()           # creates .code-review-graph/wiki/ markdown pages
get_wiki_page_tool(community_name="search")  # get specific community wiki page

Wiki pages describe each community: its purpose, key functions, dependencies, and architecture notes. Useful for onboarding and documentation.

Step 7: Embed for Semantic Search (Optional)

embed_graph_tool()    # generate vector embeddings (requires sentence-transformers)

After embedding, semantic_search_nodes_tool uses vector similarity instead of keyword matching — much better results for fuzzy queries like "authentication flow" or "database connection".

Patterns for Common Questions

"What's the high-level architecture?"

get_architecture_skeleton(level="containers")        # C4 containers view
→ get_architecture_skeleton(level="components:auth")  # drill into specific module
→ get_architecture_overview_tool()                    # coupling between communities

"How does X work?"

semantic_search_nodes_tool(query="X")
→ get_flow_tool(flow_name="X_entrypoint")
→ query_graph_tool(pattern="callees_of", target="X_main_function")

"What does module Y do?"

query_graph_tool(pattern="children_of", target="path/to/module.py")
→ get_community_tool(community_name="Y")
→ get_wiki_page_tool(community_name="Y")

"Where are the largest/most complex functions?"

find_large_functions_tool(min_lines=50, kind="Function")
audit_workspace_tool(limit=20)    # dead code + large functions + cycles; start with limit=20
# Full audit without limit can return 100KB+ — always use limit= for initial exploration

"Is there circular dependency between A and B?"

audit_workspace_tool(include_cycles=True, include_dead_code=False, include_large_functions=False)

"What's the overall health of this codebase?"

audit_workspace_tool()    # comprehensive: dead code, large functions, import cycles
→ get_architecture_overview_tool()   # coupling between communities

Tool Selection: MCP vs Direct Tools

Do NOT use MCP for everything. Use the right tool for each job:

Need	Best tool	Why
Find function declarations + signatures	semantic_search_nodes_tool	Returns params, line_end, id in one call
Find 3+ symbols at once	semantic_search_nodes_tool(query="a b c")	Single FTS5 OR query
Find all callers/usages of a symbol	query_graph_tool(callers_of)	Graph edge traversal
Search inside function bodies	Grep / ripgrep	MCP only indexes declarations, not bodies
Find a specific pattern/string in code	Grep	MCP cannot search body content
Find all places variable X is used	LSP find_references	Semantic, not text-based
Find where a value flows	trace_dataflow_tool	Graph traversal
Read a specific function body	Read(offset=line_start, limit=line_end-line_start+1)	Use line_end from MCP search first

MCP semantic_search ≈ grep "^def " + auto-read of signature lines. It does NOT replace grep for searching inside function bodies.

Tips

• list_graph_stats_tool shows last_updated — if stale, run build_or_update_graph_tool()
• query_graph_tool results include id + qualified_name — use directly in task linking
• find_files_by_pattern_tool supports glob patterns: **/*.py, !tests/**
• Communities are automatically named by dominant file paths — search by partial name
• For new codebases, run embed_graph_tool once for much better semantic search quality
• Always use line_end from search results to scope Read calls — never read whole files to find function boundaries
• list_communities_tool and get_architecture_overview_tool default to exclude_tests=True — test communities are hidden unless you pass exclude_tests=False
• semantic_search_nodes_tool defaults to exclude_tests=True — test helpers are filtered automatically
• query_graph_tool with exclude_tests=True filters BOTH results AND edges — test caller edges are suppressed, not just test nodes in results
• list_flows_tool(sort_by="criticality") surfaces helper functions (many callers) not user-facing entry points — use sort_by="depth" for actual CLI/MCP entry points
• get_architecture_skeleton() is the fastest orientation tool — 20 lines of C4 DSL vs hundreds of nodes from get_architecture_overview_tool
• get_project_standards() without arguments lists available sections; with section="patterns" returns specific content
• The C4 skeleton has [AUTO] sections (from code graph) and [FEATURE] sections (from LLM design) — designed_features field in the response lists active design work