indexion search — Codebase Search & Exploration

Find what you need in a codebase. This skill covers every search intent — pattern matching, structural queries, semantic similarity, file-level exploration, and purpose-based function lookup — and tells you which tool to reach for based on what you're actually trying to do.

Start Here: What Are You Looking For?

Don't pick a command first. Start with your intent.

"Where is X defined / used?"

You know the name. You need to find it.

Exact name match — Ident:X matches the exact token text. Finds definitions and all call sites:

# Find a type definition and all references
indexion grep "TypeIdent:DigestManifest" src/

# Find only the function definition (fn keyword + identifier)
indexion grep "fn Ident:parse_config" cmd/

# Find both definition and call sites (Ident without fn)
indexion grep "Ident:parse_config" cmd/

# List all pub struct definitions
indexion grep "pub struct *" src/

Substring match — --semantic=name:X matches as a substring. Use when you don't remember the exact name:

# Find all functions containing "build_graph" (matches build_graph_from_source too)
indexion grep --semantic=name:build_graph src/ cmd/

# Find all functions containing "sort"
indexion grep --semantic=name:sort src/

Ident:build_graph only matches a token with exactly that text. To find build_graph_from_source, use --semantic=name:build_graph instead.

Token-level search — indexion grep is not text grep. It searches over the token structure defined by KGF specs. pub fn * matches the keyword pub, the keyword fn, then any identifier — it won't match pub fn inside a string literal or comment.

Pattern syntax:

Output control:

# File paths only (like grep -l)
indexion grep --files "pub fn *" src/

# Match count per file (like grep -c)
indexion grep --count "pub fn *" src/

# Context lines around matches
indexion grep --context=3 "for ... for" src/

# Filter by file pattern
indexion grep --include='*.mbt' --exclude='*_test.mbt' "pub fn *" src/

"Find code that does X" (by description)

You don't know the name. You know what it does.

Two tools serve this intent, with a key trade-off:

One-off (no build step):

# Find functions that parse JSON configuration
indexion grep --semantic="similar:parse JSON configuration" src/

# Find error handling patterns
indexion grep --semantic="similar:handle error and return result" src/

# Find tokenization-related code
indexion grep --semantic="similar:tokenize source code into tokens" src/

Results are ranked by cosine similarity. Use descriptive phrases — "parse JSON configuration" works better than just "json".

Repeated queries (cached index):

# First: build the index (once, then incremental updates)
indexion digest build src/

# Then: query by purpose
indexion digest query "parse configuration file"
indexion digest query "calculate similarity between two texts"
indexion digest query "walk directory tree and collect files"

digest query auto-updates the index if source files have changed since the last build — you don't need to manually rebuild. See Index Lifecycle for details.

Full-text semantic search (code + wiki + docs):

# Search across everything — code, wiki pages, documentation
indexion search "how does the KGF parser work" src/ .indexion/wiki/

# Filter by attributes
indexion search --filter="node_type:code" "tokenizer" src/
indexion search --filter="language:moonbit" "parse" src/

# File paths only
indexion search --files "configuration parsing" src/

# JSON output for scripting
indexion search --json "error handling" src/

# Control result count and minimum relevance
indexion search --top-k=50 --min-score=0.1 "similarity" src/

search differs from digest query: it searches across file content (not just function purpose), and can include wiki pages and documentation. digest query is function-granular and purpose-indexed.

"Find structural patterns" (code smells, complexity)

You're looking for a shape of code, not specific text.

# Nested for loops (O(n^2) candidates)
indexion grep "for ... for" src/

# Undocumented public API
indexion grep --undocumented src/

# Functions longer than 50 lines
indexion grep --semantic=long:50 src/

# Functions shorter than 3 lines (trivial?)
indexion grep --semantic=short:3 src/

# Functions with 4+ parameters (complexity smell)
indexion grep --semantic=params-gte:4 src/

# Proxy functions (wrappers that just delegate)
indexion grep --semantic=proxy src/

# Functions by name substring
indexion grep --semantic=name:sort src/
indexion grep --semantic=name:parse src/

These are semantic queries — they analyze function structure, not just text. --semantic=proxy examines whether a function body is a single forwarded call. --semantic=long:50 counts lines of the function body.

Combining for code review:

# Post-commit quality check
indexion grep "for ... for" src/                    # O(n^2) hotspots
indexion grep --undocumented src/                    # Missing docs
indexion grep --semantic=proxy src/                  # Unnecessary wrappers
indexion grep --semantic=long:50 src/                # Overly long functions
indexion grep --semantic=params-gte:4 src/           # Complex signatures

"Which files are similar to each other?"

You want to understand overlap and relationships across files.

# Quick similarity scan — sorted pairs above threshold
indexion explore --format=list --threshold=0.7 \
  --include='*.mbt' --exclude='*moon.pkg*' src/

# Cluster similar files together
indexion explore --format=cluster --threshold=0.6 src/

# Full similarity matrix (small file sets only)
indexion explore --format=matrix src/module_a/ src/module_b/

# JSON for scripting
indexion explore --format=json --threshold=0.5 src/

# Compare specific files
indexion explore file_a.mbt file_b.mbt --threshold=0

# Function-level structural comparison (slower, more precise)
indexion explore --strategy=apted --format=list src/
indexion explore --strategy=tsed --format=list src/

# Statistical correction for large codebases
indexion explore --fdr=0.05 --format=list --threshold=0.5 src/

Strategies — when the default isn't enough:

Noise reduction tips:

• --exclude='*moon.pkg*' — package config files all look alike
• --exclude='*_wbtest.mbt' — test files share boilerplate
• Files at 40-60% with no structural overlap are "concept neighbors" — they share vocabulary because they work in the same domain (see indexion-refactor skill)

"Compare two specific texts"

Direct pairwise similarity between two texts or files.

# Compare two texts
indexion sim "hello world" "hello there"

# Compare file contents (shell reads)
indexion sim "$(cat a.mbt)" "$(cat b.mbt)"

# Choose strategy
indexion sim --strategy=ncd "text1" "text2"
indexion sim --strategy=tfidf "text1" "text2"

# Output control
indexion sim --output=similarity "text1" "text2"   # 0.0-1.0 only
indexion sim --output=distance "text1" "text2"     # distance only
indexion sim --output=both "text1" "text2"         # both (default)

"Trace references before refactoring"

Before moving or renaming something, find all references.

# All references to a type (definition + usage sites)
indexion grep "TypeIdent:DigestManifest" src/ cmd/

# All references to a function (definition + call sites) — Ident:X is exact match
indexion grep "Ident:parse_config" cmd/

# Substring match when you only know part of the name
indexion grep --semantic=name:build_graph src/ cmd/

# Verify no references to the old name remain after a rename
indexion grep "Ident:old_function_name" src/ cmd/

Note: Ident:X and TypeIdent:X are different token kinds. Type names use TypeIdent, variable/function names use Ident. When unsure, use --semantic=name:X which matches regardless of token kind.

Index Lifecycle

digest and search build cached indexes for fast repeated queries. These indexes can become stale when source files change.

How Drift Detection Works

The digest index maintains a manifest at .indexion/digest/ that tracks:

When you run digest query, it automatically compares current file hashes against the manifest. If files have changed, it incrementally re-indexes only the affected functions — no full rebuild needed.

Check Index Health

# Show what has changed since the last index build
indexion digest status src/

# Show index statistics (size, function count, providers)
indexion digest stats

digest status reports:

• Modified files (content hash differs)
• New files (not in manifest)
• Deleted files (in manifest but gone from disk)
• Estimated affected functions

When to Rebuild vs. Incremental Update

Keep Index Fresh During Development

After significant code changes (new module, major refactor), run:

# Check what's stale
indexion digest status src/

# If many changes: explicit build (faster than auto-update during query)
indexion digest build src/

# Verify
indexion digest stats

For wiki search indexes, rebuild with:

indexion wiki index build --full --wiki-dir=.indexion/wiki

Choosing the Right Tool

Common Pitfalls

"grep found nothing but I know it exists"

• Token kind mismatch: Ident:Config won't match TypeIdent:Config. When unsure of the kind, use --semantic=name:Config (matches any kind, substring).
• Exact vs substring: Ident:build_graph won't match build_graph_from_source. For substring matching, use --semantic=name:build_graph.
• Wrong target directory: Check that you're searching the right path. You can specify multiple directories: src/ cmd/.

"explore shows 95% similarity between types.mbt files"

• Type definition files share structural patterns (pub struct + getters). This inflates TF-IDF scores. It's structural similarity, not duplication. Exclude with --exclude='*types.mbt' or use --strategy=apted for function-level.

"digest query returns irrelevant results"

• Use descriptive purpose phrases, not code keywords. "calculate text similarity using TF-IDF" beats "tfidf".
• Check digest status — the index may be stale.

"search is slow on a large codebase"

• Build a digest index first: indexion digest build src/
• Use --include to narrow scope: indexion search --include='*.mbt' "query" src/

"... in grep matches too much"

• ... is non-greedy — it matches the shortest span. for ... for finds the closest pair of for loops, not the furthest. This is usually correct for nesting detection.