Magellan - Multi-language codebase mapping tool
Usage:
magellan <command> [arguments]
magellan --help
magellan --backends Show available storage backends and features
magellan watch --root <DIR> --db <FILE> [--debounce-ms <N>] [--scan-initial] [--watch-only] [--validate] [--validate-only]
magellan export --db <FILE> [--format json|jsonl|csv|scip|dot|lsif] [--output <PATH>] [--minify] [--cluster]
magellan backfill --db <FILE>
magellan index --db <FILE> --file <PATH> [--root <DIR>]
magellan delete --db <FILE> --file <PATH> [--root <DIR>]
magellan cross-file-refs --db <FILE> --fqn <FQN> [--output <FORMAT>]
magellan status --db <FILE>
magellan query --db <FILE> --file <PATH> [--kind <KIND>]
magellan find --db <FILE> (--name <NAME> | --symbol-id <ID> | --ambiguous <NAME>) [--path <PATH>] [--first]
magellan refs --db <FILE> --name <NAME> [--path <PATH>] [--direction <in|out>] [--output <FORMAT>]
magellan get --db <FILE> --file <PATH> --symbol <NAME>
magellan get-file --db <FILE> --file <PATH>
magellan chunks --db <FILE> [--limit N] [--file PATTERN] [--kind KIND] [--output FORMAT]
magellan chunk-by-span --db <FILE> --file <PATH> --start <N> --end <N> [--output FORMAT]
magellan chunk-by-symbol --db <FILE> --symbol <NAME> [--file PATTERN] [--output FORMAT]
magellan files --db <FILE> [--symbols] [--output <FORMAT>]
magellan label --db <FILE> [--label <LABEL>]... [--list] [--count] [--show-code]
magellan collisions --db <FILE> [--field <fqn|display_fqn|canonical_fqn>] [--limit <N>] [--output <FORMAT>]
magellan migrate --db <FILE> [--dry-run] [--no-backup] [--output <FORMAT>]
magellan migrate-backend --input <DB> --output <DB> [--export-dir <DIR>] [--dry-run] [--output <FORMAT>]
magellan verify --root <DIR> --db <FILE>
magellan refresh --db <FILE> [--dry-run] [--include-untracked] [--staged] [--unstaged] [--force] [--output <FORMAT>]
magellan ast --db <FILE> --file <PATH> [--position <OFFSET>] [--output <FORMAT>]
magellan find-ast --db <FILE> --kind <KIND> [--output <FORMAT>]
magellan reachable --db <FILE> --symbol <SYMBOL_ID> [--reverse] [--output <FORMAT>]
magellan dead-code --db <FILE> --entry <SYMBOL_ID> [--output <FORMAT>]
magellan cycles --db <FILE> [--symbol <SYMBOL_ID>] [--output <FORMAT>]
magellan condense --db <FILE> [--members] [--output <FORMAT>]
magellan paths --db <FILE> --start <SYMBOL_ID> [--end <SYMBOL_ID>] [--max-depth <N>] [--max-paths <N>] [--output <FORMAT>]
magellan slice --db <FILE> --target <SYMBOL_ID> [--direction <backward|forward>] [--verbose] [--output <FORMAT>]
magellan source-inventory --db <FILE> [--scan <DIR> <KIND>] [--kind <KIND>] [--list] [--stale] [--output <FORMAT>]
magellan candidate-fact submit --db <FILE> --from-source <ID> --subject-type <TYPE> --subject-key <KEY> --predicate <PRED> [--object-type <TYPE>] [--object-key <KEY>] [--properties <JSON>] [--output <FORMAT>]
magellan candidate-fact validate --db <FILE> --candidate-id <ID> [--output <FORMAT>]
magellan candidate-fact list --db <FILE> [--status <STATUS>] [--limit <N>] [--output <FORMAT>]
magellan candidate-fact review-queue --db <FILE> [--limit <N>] [--output <FORMAT>]
magellan context build --db <FILE>
magellan context summary --db <FILE>
magellan context list --db <FILE> [--kind <KIND>] [--page <N>] [--project <NAME>] [--output <FORMAT>]
magellan context symbol --db <FILE> --name <NAME> [--callers] [--callees] [--with-source] [--depth <N>] [--output <FORMAT>]
magellan context file --db <FILE> --path <PATH>
magellan context impact --db <FILE> --name <NAME> [--file <PATH>] [--depth <N>] [--output <FORMAT>]
magellan context affected --db <FILE> --name <NAME> [--file <PATH>] [--depth <N>] [--output <FORMAT>]
magellan hopgraph --db <FILE> <QUERY> [--k <N>] [--output <FORMAT>]
Commands:
watch Watch directory and index changes
backfill Recompute all metrics and derived data
index Index a single source file
delete Remove a file from the index
cross-file-refs Show references to a symbol from other files
registry Discover and list Magellan databases (scan, list)
catalog Enumerate all indexed databases with schema + capabilities
export Export graph data to JSON/JSONL/CSV/SCIP
status Show database statistics
features Show active Cargo features from project metadata
query List symbols in a file
find Find a symbol by name
refs Show calls for a symbol
get Get source code for a specific symbol
get-file Get all source code chunks for a file
chunks List all code chunks in database
chunk-by-span Get chunk by file path and byte range
chunk-by-symbol Get all chunks for a symbol name
files List all indexed files
label Query symbols by label (language, kind, etc.)
collisions List ambiguous symbol groups for a chosen field
migrate Upgrade database to current schema version
migrate-backend Migrate database between SQLite backends
verify Verify database vs filesystem
refresh Refresh index from git changes
ast Query AST nodes for a file
find-ast Find AST nodes by kind
reachable Show symbols reachable from a given symbol
dead-code Find dead code unreachable from an entry point
cycles Detect strongly connected components (cycles) in the call graph
condense Show call graph condensation (SCCs collapsed into supernodes)
paths Enumerate execution paths between symbols
slice Program slicing (backward/forward) from a target symbol
source-inventory Scan wiki/message files for graph memory source inventory
candidate-fact Submit, validate, and manage candidate facts for graph memory
context Code context queries for LLM consumption (build, summary, list, symbol, file, impact, affected)
hopgraph Embedding-based semantic symbol search (nomic-embed-text via ollama)
Global arguments:
--output <FORMAT> Output format: human (default), json (compact), or pretty (formatted)
Watch arguments:
--root <DIR> Directory to watch recursively
--db <FILE> Path to sqlitegraph database
--debounce-ms <N> Debounce delay in milliseconds (default: 500)
--watch-only Watch for changes only; skip initial directory scan baseline
--scan-initial Scan directory for source files on startup (default: true; disabled by --watch-only)
--gitignore-aware Enable .gitignore filtering (default: true)
--no-gitignore Disable .gitignore filtering (index all files)
--validate Enable pre-run and post-run validation checks
--validate-only Run validation without indexing (pre + post validation, no watch)
Export arguments:
--db <FILE> Path to sqlitegraph database
--format <FORMAT> Export format: json (default), jsonl, csv, scip, dot, or lsif
--output <PATH> Write to file instead of stdout
--minify Use compact JSON (no pretty-printing)
--no-symbols Exclude symbols from export
--no-references Exclude references from export
--no-calls Exclude calls from export
--include-collisions Include collision groups (JSON only)
--collisions-field <FIELD> Collision field: fqn, display_fqn, canonical_fqn (default: fqn)
Status arguments:
--db <FILE> Path to sqlitegraph database
Backfill arguments:
--db <FILE> Path to sqlitegraph database
Index arguments:
--db <FILE> Path to sqlitegraph database
--file <PATH> File path to index (alias: --path)
--root <DIR> Project root directory (optional)
Delete arguments:
--db <FILE> Path to sqlitegraph database
--file <PATH> File path to delete from index (alias: --path)
--root <DIR> Project root directory (optional)
Cross-file-refs arguments:
--db <FILE> Path to sqlitegraph database
--fqn <FQN> Fully qualified symbol name
--output <FORMAT> Output format: human (default), json, or pretty
Query arguments:
--db <FILE> Path to sqlitegraph database
--file <PATH> File path to query (alias: --path)
--kind <KIND> Filter by symbol kind (optional)
--with-context Include source code context lines
--with-callers Include caller references
--with-callees Include callee references
--with-semantics Include symbol kind and language
--with-checksums Include content checksums
--context-lines <N> Number of context lines (default: 3, max: 100)
Find arguments:
--db <FILE> Path to sqlitegraph database
--name <NAME> Symbol name to find
--symbol-id <ID> Stable SymbolId for precise lookup
--ambiguous <NAME> Show all candidates for ambiguous display name
--first Use first match when ambiguous (deprecated)
--path <PATH> Limit search to specific file (optional)
Refs arguments:
--db <FILE> Path to sqlitegraph database
--name <NAME> Symbol name to query
--symbol-id <ID> Use SymbolId instead of name for precise lookup
--path <PATH> File path containing the symbol
--direction <in|out> Show incoming (in) or outgoing (out) calls (default: in)
--with-context Include source code context lines
--with-semantics Include symbol kind and language
--with-checksums Include content checksums
--context-lines <N> Number of context lines (default: 3, max: 100)
Get arguments:
--db <FILE> Path to sqlitegraph database
--file <PATH> File path containing the symbol (alias: --path)
--symbol <NAME> Symbol name to retrieve
--with-context Include source code context lines
--with-semantics Include symbol kind and language
--with-checksums Include content checksums
--context-lines <N> Number of context lines (default: 3, max: 100)
Get-file arguments:
--db <FILE> Path to sqlitegraph database
--file <PATH> File path to retrieve code for (alias: --path)
Chunks arguments:
--db <FILE> Path to sqlitegraph database
--limit N Limit number of chunks returned
--file PATTERN Filter by file path pattern (substring match, alias: --path)
--kind KIND Filter by symbol kind (fn, struct, method, class, etc.)
Chunk-by-span arguments:
--db <FILE> Path to sqlitegraph database
--file <PATH> File path containing the chunk (required, alias: --path)
--start N Byte offset where chunk starts (required)
--end N Byte offset where chunk ends (required)
Chunk-by-symbol arguments:
--db <FILE> Path to sqlitegraph database
--symbol <NAME> Symbol name to find (required)
--file PATTERN Filter by file path pattern (optional, alias: --path)
Files arguments:
--db <FILE> Path to sqlitegraph database
--symbols Show symbol count per file
Label arguments:
--db <FILE> Path to sqlitegraph database
--label <LABEL> Label to query (can specify multiple for AND semantics)
--list List all available labels with counts
--count Count entities with specified label(s)
--show-code Show source code for each matching symbol
Migrate arguments:
--db <FILE> Path to sqlitegraph database
--dry-run Check version without migrating
--no-backup Skip backup creation
--output <FORMAT> Output format: human (default), json (compact), or pretty (formatted)
Backend migration arguments:
--input <DB> Path to input database (SQLite)
--output <DB> Path to output database (SQLite)
--export-dir <DIR> Directory for snapshot files (default: temp dir)
--dry-run Show what would be migrated without doing it
Verify arguments:
--root <DIR> Directory to verify against
--db <FILE> Path to sqlitegraph database
Refresh arguments:
--db <FILE> Path to sqlitegraph database
--dry-run Preview changes without applying them
--include-untracked Include untracked files in the refresh
--staged Only process staged changes
--unstaged Only process unstaged changes
--force Force re-index all tracked files
--output <FORMAT> Output format: human (default), json, or pretty
Slice arguments:
--db <FILE> Path to sqlitegraph database
--target <ID> Target symbol ID to slice from
--direction <DIR> Slice direction: backward (default) or forward
--verbose Show detailed statistics
Context arguments:
--db <FILE> Path to sqlitegraph database (or directory for multi-DB)
Context build arguments:
--db <FILE> Path to sqlitegraph database
Context summary arguments:
--db <FILE> Path to sqlitegraph database
Context list arguments:
--db <FILE> Path to sqlitegraph database
--kind <KIND> Filter by symbol kind (optional)
--page <N> Page number (default: 1)
--project <NAME> Filter to single project (optional)
--output <FORMAT> Output format: human (default), json, or pretty
Context symbol arguments:
--db <FILE> Path to sqlitegraph database
--name <NAME> Symbol name to look up (required)
--file <PATH> Limit to specific file (optional)
--callers Include caller references
--callees Include callee references
--with-source Include source code snippet
--depth <N> Recursive lookup depth (default: 1)
--project <NAME> Filter to single project (optional)
--output <FORMAT> Output format: human (default), json, or pretty
Context file arguments:
--db <FILE> Path to sqlitegraph database
--path <PATH> File path to analyze (required)
Context impact arguments:
--db <FILE> Path to sqlitegraph database
--name <NAME> Symbol name to analyze (required)
--file <PATH> Limit to specific file (optional)
--depth <N> Max traversal depth (default: 3)
--project <NAME> Filter to single project (optional)
--output <FORMAT> Output format: human (default), json, or pretty
Context affected arguments:
--db <FILE> Path to sqlitegraph database
--name <NAME> Symbol name to analyze (required)
--file <PATH> Limit to specific file (optional)
--depth <N> Max traversal depth (default: 3)
--project <NAME> Filter to single project (optional)
--output <FORMAT> Output format: human (default), json, or pretty
Navigate arguments:
<TASK> Natural-language task or question (required)
--db <FILE> Path to sqlitegraph database
--depth <N> Impact/affected traversal depth (default: 2)
--budget <N> Token budget for concise mode output (default: 4000)
--limit <N> Max symbols per term (default: 5)
--concise Single bundled context for top symbol, truncated to --budget
--with-llmgrep Also run llmgrep semantic search
--with-mirage Also run mirage CFG for top symbols
Hopgraph arguments:
<QUERY> Natural-language query (required)
--db <FILE> Path to sqlitegraph database
--k <N> Number of results to return (default: 10)
--output <FORMAT> Output format: human (default), json, pretty