Searching Codebases

Searching Codebases

Find code in any codebase by pattern or concept. One entry point, two

search strategies, automatic routing.

Prerequisites

uv tool install ripgrep

tree-sitting installs automatically when needed — for --expand context

expansion and for the binding-resolved --refs/--def/--hover tier, which

uses it to resolve symbol positions. Only the bare tree-sitter package is

fetched; the language grammars ship bundled.

Primary Command

SKILL_DIR=/mnt/skills/user/searching-codebases

python3 $SKILL_DIR/scripts/search.py SOURCE "query1" ["query2" ...] [OPTIONS]

SOURCE is any of:

• Local directory path
• GitHub URL (downloads tarball automatically)
• uploads (uses /mnt/user-data/uploads/)
• project (uses /mnt/project/)
• Path to a .zip or .tar.gz archive

Search Modes

Regex mode (patterns, identifiers, literal text):

python3 $SKILL_DIR/scripts/search.py ./repo "def handle_error"
python3 $SKILL_DIR/scripts/search.py ./repo "class.*Exception" --regex
python3 $SKILL_DIR/scripts/search.py ./repo "TODO|FIXME|HACK"

Semantic mode (concepts, natural language):

python3 $SKILL_DIR/scripts/search.py ./repo "retry logic with backoff" --semantic
python3 $SKILL_DIR/scripts/search.py ./repo "authentication flow"
python3 $SKILL_DIR/scripts/search.py ./repo "error handling strategy"

Auto-detection: short queries and code-like tokens → regex. Multi-word

natural language → semantic. Override with --regex or --semantic.

Binding-resolved mode (Python only — pyright via the python-lsp skill):

python3 $SKILL_DIR/scripts/search.py ./repo --refs SYMBOL    # find all real uses
python3 $SKILL_DIR/scripts/search.py ./repo --def SYMBOL     # go-to-definition
python3 $SKILL_DIR/scripts/search.py ./repo --hover SYMBOL   # inferred type/signature

Regex mode matches *text*, so a cross-reference for a function false-positives

on shadowed and same-named-but-unrelated symbols. --refs is binding-resolved:

pyright excludes the unrelated same-named symbol and follows imports. Use it when

you need a true "find all callers/users" for a .py symbol, not a text grep.

The tier is engaged lazily — pyright's index cost is paid only when you ask

for --refs/--def/--hover, never on ordinary searches. It is Python-only;

for non-.py sources, or when pyright/node is unavailable, it prints a one-line

degradation note and falls back to the regex text path. Each takes a single bare

symbol name and is mutually exclusive with the other two and with text queries.

Options

• --regex / --semantic: Force search mode
• --refs SYMBOL / --def SYMBOL / --hover SYMBOL: Binding-resolved Python

queries via pyright (see Binding-resolved mode above)

• --expand: Return full function bodies via tree-sitting AST context
• --benchmark: Compare indexed regex vs brute-force ripgrep
• --branch NAME: Git branch for GitHub URLs (default: main)
• --skip DIRS: Comma-separated directories to skip
• --json: Machine-readable output
• -v: Show index stats and query routing decisions

How It Works

Regex search builds a sparse n-gram inverted index over all files.

Queries are decomposed into literal fragments, looked up in the index

to identify candidate files (typically 90-99% reduction), then verified

with ripgrep. Frequency-weighted n-grams make rare character sequences

more selective.

Semantic search builds a TF-IDF index over code chunks (functions,

classes, structural entries). Queries are ranked by cosine similarity.

Context expansion (--expand) uses tree-sitting's AST cache to

identify function/class boundaries, returning complete structural units

rather than line fragments. On first use, tree-sitting scans the repo

(~700ms for 250 files); subsequent expansions are sub-millisecond.

Small codebases (< 20 files) skip indexing entirely — direct ripgrep is

faster when there's nothing to narrow.

Mixed Queries

Multiple queries can use different modes in a single invocation. Each query

is auto-routed independently, and indexes are built once per mode:

python3 $SKILL_DIR/scripts/search.py ./repo \
  "class.*Error" \
  "error recovery strategy" \
  "def retry"

Dependencies

• tree-sitting: Provides AST context expansion for --expand *and* the

symbol→position resolution that seeds the binding-resolved tier

(--refs/--def/--hover). Auto-installs the bare tree-sitter package

when either is used (grammars are bundled). Regex and semantic search work

without it.

• ripgrep: Required for regex verification. Install via uv tool install ripgrep.
• scikit-learn: Required for semantic mode. Installs automatically.
• python-lsp: Provides the binding-resolved tier (--refs/--def/--hover).

Self-bootstraps pyright on first use and requires system node (v18+). Not

required — without it those flags degrade to the regex text path.

When to Use — narrow, by design

The ONE recommended use: binding-resolved Python symbol queries.

• "find all callers of X" / "where is X really defined" for a .py

symbol, when same-named-but-unrelated symbols would pollute a text grep.

Empirical basis: rg get on psf/requests returned 232 hits, 224 of them

false; --refs get excluded all 224 (2026-06-15).

When NOT to Use — which is most of the time

Everything else. Measured head-to-head on real issue-localization tasks

(7 scikit-learn issues with merged fix-PRs, gold = PR diff files,

2026-07-04, replicating the file-discovery metric of arXiv:2602.11988):

• Literal tokens / identifiers: naive rg -l tied or beat the indexed

tier on recall@10 in every instance, at 0.4s vs 25s.

• Concept / natural-language search: the TF-IDF semantic tier never

beat identifier grep — not even on identifier-poor issues, which are

themselves rare (~0.3% of merged-PR traffic in the sample).

• First encounter / "what is this repo": use exploring-codebases.
• Repos under ~20 files: read them.

The self-test before invoking: would plain rg return the same answer?

If yes, use rg. The indexed-regex and semantic tiers are retained for

completeness and for corpora where they may yet earn their cost (very

large repos, non-code document collections), but they carry the burden

of proof.

Files

• scripts/search.py — Entry point, query routing, output formatting
• scripts/resolve.py — Input source resolution (GitHub, uploads, archives)
• scripts/context.py — tree-sitting-based AST context expansion
• scripts/ngram_index.py — Sparse n-gram inverted index, regex decomposition
• scripts/sparse_ngrams.py — Core n-gram algorithms, frequency weights
• scripts/code_rag.py — TF-IDF semantic search over code chunks
• scripts/lsp_refs.py — Binding-resolved Python tier: symbol→position

resolution (tree-sitting), pyright queries (python-lsp), soft fallback