feat: add fts indexing

Makefile

@@ -6,7 +6,7 @@ build:
 	go build -o codexis .
 
 generate-schema:
-	@sed 's/^/-- /' db/schema.sql > extension/schema.sql
+	cp db/schema.sql extension/schema.sql
 	@echo "Generated extension/schema.sql"
 
 clean:

db/fts.go

@@ -0,0 +1,76 @@
+package db
+
+import (
+	"context"
+	"strings"
+)
+
+// UpsertFileContent replaces the FTS content for a given file_id.
+func (q *Queries) UpsertFileContent(ctx context.Context, fileID int64, content string) error {
+	// Delete existing content for this file
+	if _, err := q.db.ExecContext(ctx, `DELETE FROM file_contents WHERE file_id = ?`, fileID); err != nil {
+		return err
+	}
+	// Insert new content
+	_, err := q.db.ExecContext(ctx, `INSERT INTO file_contents (file_id, content) VALUES (?, ?)`, fileID, content)
+	return err
+}
+
+// DeleteFileContentByFileID removes FTS content for a file.
+func (q *Queries) DeleteFileContentByFileID(ctx context.Context, fileID int64) error {
+	_, err := q.db.ExecContext(ctx, `DELETE FROM file_contents WHERE file_id = ?`, fileID)
+	return err
+}
+
+// DeleteStaleFileContents removes FTS content for files not in the given path list.
+func (q *Queries) DeleteStaleFileContents(ctx context.Context, paths []string) error {
+	if len(paths) == 0 {
+		_, err := q.db.ExecContext(ctx, `DELETE FROM file_contents`)
+		return err
+	}
+	placeholders := make([]string, len(paths))
+	args := make([]interface{}, len(paths))
+	for i, p := range paths {
+		placeholders[i] = "?"
+		args[i] = p
+	}
+	query := `DELETE FROM file_contents WHERE file_id NOT IN (
+		SELECT id FROM files WHERE path IN (` + strings.Join(placeholders, ",") + `)
+	)`
+	_, err := q.db.ExecContext(ctx, query, args...)
+	return err
+}
+
+// SearchResult holds a single FTS search hit.
+type SearchResult struct {
+	FileID int64
+	Path   string
+	Snippet string
+}
+
+// SearchFileContents performs a full-text search across all file contents.
+// Returns matching file paths with a snippet of the match context.
+func (q *Queries) SearchFileContents(ctx context.Context, query string, limit int) ([]SearchResult, error) {
+	rows, err := q.db.QueryContext(ctx, `
+		SELECT fc.file_id, f.path, snippet(file_contents, 1, '>>>', '<<<', '...', 20)
+		FROM file_contents fc
+		JOIN files f ON f.id = fc.file_id
+		WHERE file_contents MATCH ?
+		ORDER BY rank
+		LIMIT ?
+	`, query, limit)
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	var results []SearchResult
+	for rows.Next() {
+		var r SearchResult
+		if err := rows.Scan(&r.FileID, &r.Path, &r.Snippet); err != nil {
+			return nil, err
+		}
+		results = append(results, r)
+	}
+	return results, rows.Err()
+}

db/models.go

@@ -17,6 +17,11 @@ type File struct {
 	IndexedAt sql.NullTime
 }
 
+type FileContent struct {
+	FileID  string
+	Content string
+}
+
 type Symbol struct {
 	ID       int64
 	FileID   int64

db/schema.sql

@@ -32,3 +32,11 @@ CREATE INDEX idx_symbols_exported ON symbols(exported, kind);
 CREATE INDEX idx_files_path ON files(path);
 CREATE INDEX idx_files_language ON files(language);
 CREATE INDEX idx_files_package ON files(package);
+
+-- FTS5 virtual table for full-text search of file contents.
+-- content is stored here (not external content), keyed by file_id.
+CREATE VIRTUAL TABLE file_contents USING fts5(
+    file_id UNINDEXED,
+    content,
+    tokenize='porter unicode61'
+);

extension/codexis.ts

@@ -38,7 +38,13 @@ Example queries:
   SELECT c.name as parent, s.name, s.kind, s.line FROM symbols s JOIN symbols c ON s.parent_id=c.id WHERE c.name='AuthService'
 
   -- Overview: symbols per area
-  SELECT CASE WHEN f.path LIKE 'backend/%' THEN 'backend' WHEN f.path LIKE 'frontend/%' THEN 'frontend' ELSE 'other' END as area, COUNT(*) FROM symbols s JOIN files f ON s.file_id=f.id GROUP BY area`;
+  SELECT CASE WHEN f.path LIKE 'backend/%' THEN 'backend' WHEN f.path LIKE 'frontend/%' THEN 'frontend' ELSE 'other' END as area, COUNT(*) FROM symbols s JOIN files f ON s.file_id=f.id GROUP BY area
+
+  -- Full-text search for content across all files
+  SELECT f.path, snippet(file_contents, 1, '>>>', '<<<', '...', 20) as match FROM file_contents fc JOIN files f ON f.id=fc.file_id WHERE file_contents MATCH 'handleRequest' ORDER BY rank LIMIT 10
+
+  -- FTS search scoped to a directory
+  SELECT f.path, snippet(file_contents, 1, '>>>', '<<<', '...', 20) as match FROM file_contents fc JOIN files f ON f.id=fc.file_id WHERE file_contents MATCH 'database migration' AND f.path LIKE 'backend/%' ORDER BY rank LIMIT 10`;
 
 function findGitRoot(cwd: string): string | null {
   try {

extension/schema.sql

@@ -1,34 +1,42 @@
--- CREATE TABLE files (
+CREATE TABLE files (
---     id          INTEGER PRIMARY KEY,
+    id          INTEGER PRIMARY KEY,
---     path        TEXT    NOT NULL UNIQUE,
+    path        TEXT    NOT NULL UNIQUE,
---     language    TEXT    NOT NULL,
+    language    TEXT    NOT NULL,
---     package     TEXT,
+    package     TEXT,
---     hash        TEXT    NOT NULL,
+    hash        TEXT    NOT NULL,
---     indexed_at  DATETIME DEFAULT CURRENT_TIMESTAMP
+    indexed_at  DATETIME DEFAULT CURRENT_TIMESTAMP
--- );
+);
--- 
+
--- CREATE TABLE symbols (
+CREATE TABLE symbols (
---     id          INTEGER PRIMARY KEY,
+    id          INTEGER PRIMARY KEY,
---     file_id     INTEGER NOT NULL REFERENCES files(id) ON DELETE CASCADE,
+    file_id     INTEGER NOT NULL REFERENCES files(id) ON DELETE CASCADE,
---     name        TEXT    NOT NULL,
+    name        TEXT    NOT NULL,
---     kind        TEXT    NOT NULL CHECK(kind IN (
+    kind        TEXT    NOT NULL CHECK(kind IN (
---         'function', 'method', 'class', 'type',
+        'function', 'method', 'class', 'type',
---         'interface', 'constant', 'variable', 'constructor'
+        'interface', 'constant', 'variable', 'constructor'
---     )),
+    )),
---     line        INTEGER NOT NULL,
+    line        INTEGER NOT NULL,
---     line_end    INTEGER,
+    line_end    INTEGER,
---     col         INTEGER,
+    col         INTEGER,
---     col_end     INTEGER,
+    col_end     INTEGER,
---     exported    BOOLEAN,
+    exported    BOOLEAN,
---     parent_id   INTEGER REFERENCES symbols(id),
+    parent_id   INTEGER REFERENCES symbols(id),
---     UNIQUE(file_id, name, kind, line)
+    UNIQUE(file_id, name, kind, line)
--- );
+);
--- 
+
--- CREATE INDEX idx_symbols_name ON symbols(name);
+CREATE INDEX idx_symbols_name ON symbols(name);
--- CREATE INDEX idx_symbols_kind ON symbols(kind);
+CREATE INDEX idx_symbols_kind ON symbols(kind);
--- CREATE INDEX idx_symbols_file_line ON symbols(file_id, line);
+CREATE INDEX idx_symbols_file_line ON symbols(file_id, line);
--- CREATE INDEX idx_symbols_parent ON symbols(parent_id);
+CREATE INDEX idx_symbols_parent ON symbols(parent_id);
--- CREATE INDEX idx_symbols_exported ON symbols(exported, kind);
+CREATE INDEX idx_symbols_exported ON symbols(exported, kind);
--- CREATE INDEX idx_files_path ON files(path);
+CREATE INDEX idx_files_path ON files(path);
--- CREATE INDEX idx_files_language ON files(language);
+CREATE INDEX idx_files_language ON files(language);
--- CREATE INDEX idx_files_package ON files(package);
+CREATE INDEX idx_files_package ON files(package);
+
+-- FTS5 virtual table for full-text search of file contents.
+-- content is stored here (not external content), keyed by file_id.
+CREATE VIRTUAL TABLE file_contents USING fts5(
+    file_id UNINDEXED,
+    content,
+    tokenize='porter unicode61'
+);

go.mod

@@ -3,6 +3,18 @@ module codexis
 go 1.25.0
 
 require (
-	github.com/mattn/go-sqlite3 v1.14.42
 	github.com/odvcencio/gotreesitter v0.13.4
+	modernc.org/sqlite v1.48.2
+)
+
+require (
+	github.com/dustin/go-humanize v1.0.1 // indirect
+	github.com/google/uuid v1.6.0 // indirect
+	github.com/mattn/go-isatty v0.0.20 // indirect
+	github.com/ncruces/go-strftime v1.0.0 // indirect
+	github.com/remyoudompheng/bigfft v0.0.0-20230129092748-24d4a6f8daec // indirect
+	golang.org/x/sys v0.42.0 // indirect
+	modernc.org/libc v1.70.0 // indirect
+	modernc.org/mathutil v1.7.1 // indirect
+	modernc.org/memory v1.11.0 // indirect
 )

go.sum

@@ -1,4 +1,53 @@
-github.com/mattn/go-sqlite3 v1.14.42 h1:MigqEP4ZmHw3aIdIT7T+9TLa90Z6smwcthx+Azv4Cgo=
+github.com/dustin/go-humanize v1.0.1 h1:GzkhY7T5VNhEkwH0PVJgjz+fX1rhBrR7pRT3mDkpeCY=
-github.com/mattn/go-sqlite3 v1.14.42/go.mod h1:pjEuOr8IwzLJP2MfGeTb0A35jauH+C2kbHKBr7yXKVQ=
+github.com/dustin/go-humanize v1.0.1/go.mod h1:Mu1zIs6XwVuF/gI1OepvI0qD18qycQx+mFykh5fBlto=
+github.com/google/pprof v0.0.0-20250317173921-a4b03ec1a45e h1:ijClszYn+mADRFY17kjQEVQ1XRhq2/JR1M3sGqeJoxs=
+github.com/google/pprof v0.0.0-20250317173921-a4b03ec1a45e/go.mod h1:boTsfXsheKC2y+lKOCMpSfarhxDeIzfZG1jqGcPl3cA=
+github.com/google/uuid v1.6.0 h1:NIvaJDMOsjHA8n1jAhLSgzrAzy1Hgr+hNrb57e+94F0=
+github.com/google/uuid v1.6.0/go.mod h1:TIyPZe4MgqvfeYDBFedMoGGpEw/LqOeaOT+nhxU+yHo=
+github.com/hashicorp/golang-lru/v2 v2.0.7 h1:a+bsQ5rvGLjzHuww6tVxozPZFVghXaHOwFs4luLUK2k=
+github.com/hashicorp/golang-lru/v2 v2.0.7/go.mod h1:QeFd9opnmA6QUJc5vARoKUSoFhyfM2/ZepoAG6RGpeM=
+github.com/mattn/go-isatty v0.0.20 h1:xfD0iDuEKnDkl03q4limB+vH+GxLEtL/jb4xVJSWWEY=
+github.com/mattn/go-isatty v0.0.20/go.mod h1:W+V8PltTTMOvKvAeJH7IuucS94S2C6jfK/D7dTCTo3Y=
+github.com/ncruces/go-strftime v1.0.0 h1:HMFp8mLCTPp341M/ZnA4qaf7ZlsbTc+miZjCLOFAw7w=
+github.com/ncruces/go-strftime v1.0.0/go.mod h1:Fwc5htZGVVkseilnfgOVb9mKy6w1naJmn9CehxcKcls=
 github.com/odvcencio/gotreesitter v0.13.4 h1:O/FqOlabRz1Neg6UISx0URtwuN1FQ2eGCc846KHcBbQ=
 github.com/odvcencio/gotreesitter v0.13.4/go.mod h1:Sx+iYJBfw5xSWkSttLSuFvguJctlH+ma1BTxZ0MPCqo=
+github.com/remyoudompheng/bigfft v0.0.0-20230129092748-24d4a6f8daec h1:W09IVJc94icq4NjY3clb7Lk8O1qJ8BdBEF8z0ibU0rE=
+github.com/remyoudompheng/bigfft v0.0.0-20230129092748-24d4a6f8daec/go.mod h1:qqbHyh8v60DhA7CoWK5oRCqLrMHRGoxYCSS9EjAz6Eo=
+golang.org/x/mod v0.33.0 h1:tHFzIWbBifEmbwtGz65eaWyGiGZatSrT9prnU8DbVL8=
+golang.org/x/mod v0.33.0/go.mod h1:swjeQEj+6r7fODbD2cqrnje9PnziFuw4bmLbBZFrQ5w=
+golang.org/x/sync v0.19.0 h1:vV+1eWNmZ5geRlYjzm2adRgW2/mcpevXNg50YZtPCE4=
+golang.org/x/sync v0.19.0/go.mod h1:9KTHXmSnoGruLpwFjVSX0lNNA75CykiMECbovNTZqGI=
+golang.org/x/sys v0.6.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
+golang.org/x/sys v0.42.0 h1:omrd2nAlyT5ESRdCLYdm3+fMfNFE/+Rf4bDIQImRJeo=
+golang.org/x/sys v0.42.0/go.mod h1:4GL1E5IUh+htKOUEOaiffhrAeqysfVGipDYzABqnCmw=
+golang.org/x/tools v0.42.0 h1:uNgphsn75Tdz5Ji2q36v/nsFSfR/9BRFvqhGBaJGd5k=
+golang.org/x/tools v0.42.0/go.mod h1:Ma6lCIwGZvHK6XtgbswSoWroEkhugApmsXyrUmBhfr0=
+modernc.org/cc/v4 v4.27.1 h1:9W30zRlYrefrDV2JE2O8VDtJ1yPGownxciz5rrbQZis=
+modernc.org/cc/v4 v4.27.1/go.mod h1:uVtb5OGqUKpoLWhqwNQo/8LwvoiEBLvZXIQ/SmO6mL0=
+modernc.org/ccgo/v4 v4.32.0 h1:hjG66bI/kqIPX1b2yT6fr/jt+QedtP2fqojG2VrFuVw=
+modernc.org/ccgo/v4 v4.32.0/go.mod h1:6F08EBCx5uQc38kMGl+0Nm0oWczoo1c7cgpzEry7Uc0=
+modernc.org/fileutil v1.4.0 h1:j6ZzNTftVS054gi281TyLjHPp6CPHr2KCxEXjEbD6SM=
+modernc.org/fileutil v1.4.0/go.mod h1:EqdKFDxiByqxLk8ozOxObDSfcVOv/54xDs/DUHdvCUU=
+modernc.org/gc/v2 v2.6.5 h1:nyqdV8q46KvTpZlsw66kWqwXRHdjIlJOhG6kxiV/9xI=
+modernc.org/gc/v2 v2.6.5/go.mod h1:YgIahr1ypgfe7chRuJi2gD7DBQiKSLMPgBQe9oIiito=
+modernc.org/gc/v3 v3.1.2 h1:ZtDCnhonXSZexk/AYsegNRV1lJGgaNZJuKjJSWKyEqo=
+modernc.org/gc/v3 v3.1.2/go.mod h1:HFK/6AGESC7Ex+EZJhJ2Gni6cTaYpSMmU/cT9RmlfYY=
+modernc.org/goabi0 v0.2.0 h1:HvEowk7LxcPd0eq6mVOAEMai46V+i7Jrj13t4AzuNks=
+modernc.org/goabi0 v0.2.0/go.mod h1:CEFRnnJhKvWT1c1JTI3Avm+tgOWbkOu5oPA8eH8LnMI=
+modernc.org/libc v1.70.0 h1:U58NawXqXbgpZ/dcdS9kMshu08aiA6b7gusEusqzNkw=
+modernc.org/libc v1.70.0/go.mod h1:OVmxFGP1CI/Z4L3E0Q3Mf1PDE0BucwMkcXjjLntvHJo=
+modernc.org/mathutil v1.7.1 h1:GCZVGXdaN8gTqB1Mf/usp1Y/hSqgI2vAGGP4jZMCxOU=
+modernc.org/mathutil v1.7.1/go.mod h1:4p5IwJITfppl0G4sUEDtCr4DthTaT47/N3aT6MhfgJg=
+modernc.org/memory v1.11.0 h1:o4QC8aMQzmcwCK3t3Ux/ZHmwFPzE6hf2Y5LbkRs+hbI=
+modernc.org/memory v1.11.0/go.mod h1:/JP4VbVC+K5sU2wZi9bHoq2MAkCnrt2r98UGeSK7Mjw=
+modernc.org/opt v0.1.4 h1:2kNGMRiUjrp4LcaPuLY2PzUfqM/w9N23quVwhKt5Qm8=
+modernc.org/opt v0.1.4/go.mod h1:03fq9lsNfvkYSfxrfUhZCWPk1lm4cq4N+Bh//bEtgns=
+modernc.org/sortutil v1.2.1 h1:+xyoGf15mM3NMlPDnFqrteY07klSFxLElE2PVuWIJ7w=
+modernc.org/sortutil v1.2.1/go.mod h1:7ZI3a3REbai7gzCLcotuw9AC4VZVpYMjDzETGsSMqJE=
+modernc.org/sqlite v1.48.2 h1:5CnW4uP8joZtA0LedVqLbZV5GD7F/0x91AXeSyjoh5c=
+modernc.org/sqlite v1.48.2/go.mod h1:hWjRO6Tj/5Ik8ieqxQybiEOUXy0NJFNp2tpvVpKlvig=
+modernc.org/strutil v1.2.1 h1:UneZBkQA+DX2Rp35KcM69cSsNES9ly8mQWD71HKlOA0=
+modernc.org/strutil v1.2.1/go.mod h1:EHkiggD70koQxjVdSBM3JKM7k6L0FbGE5eymy9i3B9A=
+modernc.org/token v1.1.0 h1:Xl7Ap9dKaEs5kLoOQeQmPWevfnk/DM5qcLcYlA8ys6Y=
+modernc.org/token v1.1.0/go.mod h1:UGzOrNV1mAFSEB63lOFHIpNRUVMvYTc6yu1SMY/XTDM=

indexer/indexer.go

@@ -15,19 +15,31 @@ import (
 	"codexis/db"
 )
 
+
+// ProgressFunc is called for each file being processed.
+// current is the 1-based index, total is the total file count, path is the file being processed.
+type ProgressFunc func(current, total int, path string)
+
+const defaultBatchSize = 100
+
 // Indexer walks a codebase, extracts symbols via tree-sitter, and stores them in SQLite.
 type Indexer struct {
+	db         *sql.DB
 	queries    *db.Queries
 	root       string
 	force      bool
+	BatchSize  int
+	OnProgress ProgressFunc
 }
 
 // New creates a new Indexer.
-func New(queries *db.Queries, root string, force bool) *Indexer {
+func New(sqlDB *sql.DB, queries *db.Queries, root string, force bool) *Indexer {
 	return &Indexer{
+		db:        sqlDB,
 		queries:   queries,
 		root:      root,
 		force:     force,
+		BatchSize: defaultBatchSize,
 	}
 }
 
@@ -47,11 +59,62 @@ func (idx *Indexer) Index(ctx context.Context) (*Stats, error) {
 	}
 
 	stats := &Stats{FilesTotal: len(files)}
+	batchSize := idx.BatchSize
+	if batchSize <= 0 {
+		batchSize = defaultBatchSize
+	}
 
-	for _, relPath := range files {
+	// Process files in transaction batches
-		indexed, symbolCount, err := idx.indexFile(ctx, relPath)
+	for batchStart := 0; batchStart < len(files); batchStart += batchSize {
+		batchEnd := batchStart + batchSize
+		if batchEnd > len(files) {
+			batchEnd = len(files)
+		}
+		batch := files[batchStart:batchEnd]
+
+		if err := idx.indexBatch(ctx, batch, batchStart, stats); err != nil {
+			return nil, fmt.Errorf("indexing batch: %w", err)
+		}
+	}
+
+	// Clean up files that no longer exist (in its own transaction)
+	tx, err := idx.db.BeginTx(ctx, nil)
 	if err != nil {
-			fmt.Fprintf(os.Stderr, "warn: %s: %v\n", relPath, err)
+		return nil, fmt.Errorf("begin cleanup tx: %w", err)
+	}
+	defer tx.Rollback()
+
+	txQueries := idx.queries.WithTx(tx)
+	if err := txQueries.DeleteStaleFileContents(ctx, files); err != nil {
+		return nil, fmt.Errorf("cleaning stale file contents: %w", err)
+	}
+	if err := txQueries.DeleteStaleFiles(ctx, files); err != nil {
+		return nil, fmt.Errorf("cleaning stale files: %w", err)
+	}
+	if err := tx.Commit(); err != nil {
+		return nil, fmt.Errorf("commit cleanup tx: %w", err)
+	}
+
+	return stats, nil
+}
+
+// indexBatch processes a slice of files within a single transaction.
+func (idx *Indexer) indexBatch(ctx context.Context, batch []string, offset int, stats *Stats) error {
+	tx, err := idx.db.BeginTx(ctx, nil)
+	if err != nil {
+		return fmt.Errorf("begin tx: %w", err)
+	}
+	defer tx.Rollback()
+
+	txQueries := idx.queries.WithTx(tx)
+
+	for i, relPath := range batch {
+		if idx.OnProgress != nil {
+			idx.OnProgress(offset+i+1, stats.FilesTotal, relPath)
+		}
+		indexed, symbolCount, err := idx.indexFile(ctx, txQueries, relPath)
+		if err != nil {
+			fmt.Fprintf(os.Stderr, "\rwarn: %s: %v\033[K\n", relPath, err)
 			continue
 		}
 		if indexed {
@@ -62,15 +125,13 @@ func (idx *Indexer) Index(ctx context.Context) (*Stats, error) {
 		}
 	}
 
-	// Clean up files that no longer exist
+	if err := tx.Commit(); err != nil {
-	if err := idx.queries.DeleteStaleFiles(ctx, files); err != nil {
+		return fmt.Errorf("commit tx: %w", err)
-		return nil, fmt.Errorf("cleaning stale files: %w", err)
 	}
-
+	return nil
-	return stats, nil
 }
 
-func (idx *Indexer) indexFile(ctx context.Context, relPath string) (indexed bool, symbolCount int, err error) {
+func (idx *Indexer) indexFile(ctx context.Context, q *db.Queries, relPath string) (indexed bool, symbolCount int, err error) {
 	absPath := filepath.Join(idx.root, relPath)
 
 	src, err := os.ReadFile(absPath)
@@ -82,7 +143,7 @@ func (idx *Indexer) indexFile(ctx context.Context, relPath string) (indexed bool
 
 	// Check if file has changed
 	if !idx.force {
-		existing, err := idx.queries.GetFileByPath(ctx, relPath)
+		existing, err := q.GetFileByPath(ctx, relPath)
 		if err == nil && existing.Hash == hash {
 			return false, 0, nil // unchanged
 		}
@@ -94,11 +155,30 @@ func (idx *Indexer) indexFile(ctx context.Context, relPath string) (indexed bool
 		return false, 0, nil
 	}
 
-	// Extract package
+	// Check if this language has a tags query — skip parsing if not
-	pkg := ExtractPackage(src, relPath, entry)
+	tagsQuery := grammars.ResolveTagsQuery(*entry)
+	hasTagsQuery := tagsQuery != ""
+
+	var tree *gotreesitter.Tree
+	if hasTagsQuery {
+		// Parse once, reuse tree for package extraction and tagging
+		lang := entry.Language()
+		parser := gotreesitter.NewParser(lang)
+		parsedTree, parseErr := parser.Parse(src)
+		if parseErr != nil {
+			return false, 0, fmt.Errorf("parsing: %w", parseErr)
+		}
+		tree = parsedTree
+		if tree != nil {
+			defer tree.Release()
+		}
+	}
+
+	// Extract package (uses tree if available, falls back to dir name)
+	pkg := ExtractPackage(src, relPath, entry, tree)
 
 	// Upsert file record
-	file, err := idx.queries.UpsertFile(ctx, db.UpsertFileParams{
+	file, err := q.UpsertFile(ctx, db.UpsertFileParams{
 		Path:     relPath,
 		Language: entry.Name,
 		Package:  sql.NullString{String: pkg, Valid: pkg != ""},
@@ -108,13 +188,22 @@ func (idx *Indexer) indexFile(ctx context.Context, relPath string) (indexed bool
 		return false, 0, fmt.Errorf("upserting file: %w", err)
 	}
 
+	// Store file content for FTS
+	if err := q.UpsertFileContent(ctx, file.ID, string(src)); err != nil {
+		return false, 0, fmt.Errorf("upserting file content: %w", err)
+	}
+
+	if !hasTagsQuery {
+		return true, 0, nil
+	}
+
 	// Clear old symbols
-	if err := idx.queries.DeleteSymbolsByFileID(ctx, file.ID); err != nil {
+	if err := q.DeleteSymbolsByFileID(ctx, file.ID); err != nil {
 		return false, 0, fmt.Errorf("deleting old symbols: %w", err)
 	}
 
 	// Extract and store symbols
-	tags := extractTags(src, entry)
+	tags := extractTags(src, entry, tree)
 	defs := buildSymbolDefs(tags, file.ID, entry.Name)
 
 	// Insert symbols in order, tracking DB IDs for parent resolution
@@ -127,7 +216,7 @@ func (idx *Indexer) indexFile(ctx context.Context, relPath string) (indexed bool
 			params.ParentID = sql.NullInt64{Int64: dbIDs[parentIdx], Valid: true}
 		}
 
-		id, err := idx.queries.InsertSymbol(ctx, params)
+		id, err := q.InsertSymbol(ctx, params)
 		if err != nil {
 			return false, 0, fmt.Errorf("inserting symbol %q: %w", params.Name, err)
 		}
@@ -137,7 +226,11 @@ func (idx *Indexer) indexFile(ctx context.Context, relPath string) (indexed bool
 	return true, len(defs), nil
 }
 
-func extractTags(src []byte, entry *grammars.LangEntry) []gotreesitter.Tag {
+func extractTags(src []byte, entry *grammars.LangEntry, tree *gotreesitter.Tree) []gotreesitter.Tag {
+	if tree == nil {
+		return nil
+	}
+
 	lang := entry.Language()
 
 	// ResolveTagsQuery returns the explicit TagsQuery if set, otherwise infers
@@ -152,7 +245,7 @@ func extractTags(src []byte, entry *grammars.LangEntry) []gotreesitter.Tag {
 		return nil
 	}
 
-	return tagger.Tag(src)
+	return tagger.TagTree(tree)
 }
 
 type symbolDef struct {

indexer/scope.go

@@ -21,16 +21,18 @@ var packageQueries = map[string]string{
 	"erlang":   `(module_attribute name: (atom) @name)`,
 }
 
-// ExtractPackage extracts the package/module name from source code.
+// ExtractPackage extracts the package/module name from a pre-parsed tree.
 // Falls back to deriving from the file path if no language-specific query exists
 // or the query finds no match.
-func ExtractPackage(src []byte, filePath string, entry *grammars.LangEntry) string {
+func ExtractPackage(src []byte, filePath string, entry *grammars.LangEntry, tree *gotreesitter.Tree) string {
 	if queryStr, ok := packageQueries[entry.Name]; ok {
+		if tree != nil && tree.RootNode() != nil {
 			lang := entry.Language()
-		if pkg := runPackageQuery(src, lang, queryStr); pkg != "" {
+			if pkg := runPackageQuery(src, lang, queryStr, tree); pkg != "" {
 				return pkg
 			}
 		}
+	}
 
 	// Fallback: derive from directory name
 	dir := filepath.Dir(filePath)
@@ -40,14 +42,7 @@ func ExtractPackage(src []byte, filePath string, entry *grammars.LangEntry) stri
 	return filepath.Base(dir)
 }
 
-func runPackageQuery(src []byte, lang *gotreesitter.Language, queryStr string) string {
+func runPackageQuery(src []byte, lang *gotreesitter.Language, queryStr string, tree *gotreesitter.Tree) string {
-	parser := gotreesitter.NewParser(lang)
-	tree, err := parser.Parse(src)
-	if err != nil || tree == nil || tree.RootNode() == nil {
-		return ""
-	}
-	defer tree.Release()
-
 	query, err := gotreesitter.NewQuery(queryStr, lang)
 	if err != nil {
 		return ""

main.go

@@ -3,27 +3,61 @@ package main
 import (
 	"context"
 	"database/sql"
-	"embed"
+	_ "embed"
 	"flag"
 	"fmt"
 	"os"
+	"os/signal"
 	"path/filepath"
+	"runtime/pprof"
+	"strings"
 	"time"
 
-	_ "github.com/mattn/go-sqlite3"
+	_ "modernc.org/sqlite"
 
 	"codexis/db"
 	"codexis/indexer"
 )
 
+
+//go:embed db/schema.sql
+var schemaSQL string
+
 const dbDir = ".codexis"
 const dbFileName = "index.db"
 
 func main() {
 	force := flag.Bool("force", false, "Force full re-index (ignore file hashes)")
 	output := flag.String("o", "", "Output database path (default: <root>/.codexis/index.db)")
+	cpuprofile := flag.String("cpuprofile", "", "Write CPU profile to file")
 	flag.Parse()
 
+	// CPU profiling
+	if *cpuprofile != "" {
+		f, err := os.Create(*cpuprofile)
+		if err != nil {
+			fmt.Fprintf(os.Stderr, "error creating profile: %v\n", err)
+			os.Exit(1)
+		}
+		pprof.StartCPUProfile(f)
+
+		// Flush profile on interrupt
+		sigCh := make(chan os.Signal, 1)
+		signal.Notify(sigCh, os.Interrupt)
+		go func() {
+			<-sigCh
+			fmt.Fprintf(os.Stderr, "\nInterrupted, flushing CPU profile...\n")
+			pprof.StopCPUProfile()
+			f.Close()
+			os.Exit(1)
+		}()
+
+		defer func() {
+			pprof.StopCPUProfile()
+			f.Close()
+		}()
+	}
+
 	root := "."
 	if flag.NArg() > 0 {
 		root = flag.Arg(0)
@@ -54,7 +88,7 @@ func main() {
 func run(root, dbPath string, force bool) error {
 	ctx := context.Background()
 
-	sqlDB, err := sql.Open("sqlite3", dbPath+"?_journal_mode=WAL&_foreign_keys=on")
+	sqlDB, err := sql.Open("sqlite", dbPath+"?_pragma=journal_mode(WAL)&_pragma=foreign_keys(1)")
 	if err != nil {
 		return fmt.Errorf("opening database: %w", err)
 	}
@@ -66,7 +100,26 @@ func run(root, dbPath string, force bool) error {
 	}
 
 	queries := db.New(sqlDB)
-	idx := indexer.New(queries, root, force)
+	idx := indexer.New(sqlDB, queries, root, force)
+
+	isTTY := fileIsTTY(os.Stderr)
+	idx.OnProgress = func(current, total int, path string) {
+		if !isTTY {
+			return
+		}
+		pct := current * 100 / total
+		barWidth := 30
+		filled := barWidth * current / total
+		bar := strings.Repeat("█", filled) + strings.Repeat("░", barWidth-filled)
+		display := path
+		if len(display) > 40 {
+			display = "..." + display[len(display)-37:]
+		}
+		fmt.Fprintf(os.Stderr, "\r  %s %3d%% (%d/%d) %s\033[K", bar, pct, current, total, display)
+		if current == total {
+			fmt.Fprintf(os.Stderr, "\r\033[K")
+		}
+	}
 
 	start := time.Now()
 	fmt.Fprintf(os.Stderr, "Indexing %s...\n", root)
@@ -86,8 +139,13 @@ func run(root, dbPath string, force bool) error {
 	return nil
 }
 
-//go:embed db/schema.sql
+func fileIsTTY(f *os.File) bool {
-var schemaSQL string
+	fi, err := f.Stat()
+	if err != nil {
+		return false
+	}
+	return fi.Mode()&os.ModeCharDevice != 0
+}
 
 func createSchema(ctx context.Context, sqlDB *sql.DB) error {
 	_, err := sqlDB.ExecContext(ctx, schemaSQL)