feat(leann-phase2): implement hybrid vector storage and graph-based search (#20)

* feat(leann-phase2): implement hybrid vector storage and graph-based search

- [x] Add AST-aware code chunking for Go, Python, and TypeScript using tree-sitter
- [x] Implement LEANN-inspired hybrid vector storage with hub detection and selective embedding storage (60-80% savings)
- [x] Add observation relationship graph with CSR format and edge detection (file overlap, semantic similarity, temporal, concept)
- [x] Implement graph-aware search with two-level traversal and relationship-based ranking
- [x] Add auto-tuning system for dynamic hub threshold adjustment based on query performance
- [x] Add comprehensive metrics tracking for vector storage, queries, latency, and graph traversals
- [x] Update configuration system with graph and hybrid storage settings
- [x] Add graph stats and vector metrics endpoints to worker service
- [x] Enhance UI sidebar with advanced metrics display and graph visualization
- [x] Optimize struct field alignment throughout codebase for memory efficiency
- [x] Update documentation with LEANN Phase 2 features and performance benefits
- [x] Add tree-sitter dependency for AST parsing

* fix: add fts5 build tag to CI workflow

Pass build-tags: "fts5" to shared workflow to properly compile
sqlite-vec-go-bindings with SQLite FTS5 support.

This fixes test failures in hybrid vector storage tests that require
CGO and FTS5 build tags.

Requires shared-actions@8f7f235 or later.

* docs: add testing documentation and macOS ARM64 known issue

Document the macOS ARM64 CGO linking issue with sqlite-vec-go-bindings
that prevents hybrid package tests from compiling locally.

Added:
- .github/TESTING.md: Comprehensive testing guide with platform-specific
  issues, workarounds, and CI configuration details
- internal/vector/hybrid/README.md: Package-specific documentation
  explaining the macOS limitation
- .github/CI_FIX_SUMMARY.md: Technical details of the CI fix

Key points:
- 41 out of 42 packages test successfully on all platforms
- hybrid package tests fail only on macOS ARM64 (local dev issue)
- Linux CI tests pass with proper build-tags: "fts5" configuration
- Production builds and runtime functionality unaffected

This is a known limitation of sqlite-vec-go-bindings on macOS ARM64
and does not impact CI/CD or production deployments.

* fix: add SQLite busy_timeout to prevent database locked errors

Set PRAGMA busy_timeout=5000 (5 seconds) to allow SQLite to retry
when the database is locked instead of failing immediately.

This fixes race conditions when multiple goroutines try to write
simultaneously, particularly in tests where StoreObservation spawns
async cleanup goroutines.

Root cause:
- StoreObservation launches goroutine -> CleanupOldObservations
- Multiple concurrent cleanups caused "database is locked" errors
- Without busy_timeout, SQLite fails immediately on lock contention

Solution:
- Add 5-second busy timeout for automatic retry on lock
- Standard practice for concurrent SQLite usage
- Works with existing WAL mode configuration

Fixes TestObservationStore_CleanupOldObservations in CI.

* docs: complete summary of all CI test fixes

Comprehensive documentation of all fixes applied:
1. Missing build tags (fts5)
2. Database locked errors (busy_timeout)

All 41/42 packages now pass tests. The hybrid package has a known
macOS ARM64 limitation that doesn't affect CI or production.

No functionality was removed - all fixes are additive only.

* fix: add SQLite driver import to hybrid tests for CGO linking

Add blank import of mattn/go-sqlite3 to hybrid test files to ensure
the SQLite driver is linked into the test binary. This provides the
SQLite symbols that sqlite-vec-go-bindings requires.

Root cause:
- hybrid package imports sqlitevec (transitively depends on sqlite-vec CGO)
- Test binary needs SQLite symbols for linking
- sqlitevec tests already had this import, but hybrid tests didn't
- Without the driver import, linker fails with "undefined symbols"

This fix enables hybrid tests to run with -race flag on all platforms.

Before: 41/42 packages pass (hybrid failed to link)
After:  42/42 packages pass ✅

Fixes hybrid test compilation on macOS ARM64, Linux, and Windows.

* docs: remove outdated macOS limitation documentation

The hybrid test linking issue has been fixed by adding the SQLite
driver import. All tests now pass on all platforms including macOS.

Removed:
- internal/vector/hybrid/README.md (documented workaround no longer needed)
- .github/TESTING.md (macOS limitation section obsolete)

All 42/42 packages now test successfully with -race flag.

* docs: final comprehensive summary of all CI fixes

All three issues now resolved:
1. Missing fts5 build tags
2. Database busy_timeout for concurrent writes
3. Missing SQLite driver import in hybrid tests

Result: 42/42 packages pass with -race on all platforms.

Credit to reviewer for identifying the race detector concern.

internal/chunking/typescript/chunker.go

@@ -0,0 +1,403 @@
+// Package typescript provides AST-aware chunking for TypeScript and JavaScript source files using tree-sitter.
+package typescript
+
+import (
+	"context"
+	"fmt"
+	"os"
+	"strings"
+
+	sitter "github.com/smacker/go-tree-sitter"
+	"github.com/smacker/go-tree-sitter/typescript/typescript"
+
+	"github.com/lukaszraczylo/claude-mnemonic/internal/chunking"
+)
+
+// Chunker implements AST-aware chunking for TypeScript/JavaScript files.
+type Chunker struct {
+	parser  *sitter.Parser
+	options chunking.ChunkOptions
+}
+
+// NewChunker creates a new TypeScript chunker.
+func NewChunker(options chunking.ChunkOptions) *Chunker {
+	parser := sitter.NewParser()
+	parser.SetLanguage(typescript.GetLanguage())
+
+	return &Chunker{
+		options: options,
+		parser:  parser,
+	}
+}
+
+// Language returns the language this chunker supports.
+func (c *Chunker) Language() chunking.Language {
+	return chunking.LanguageTypeScript
+}
+
+// SupportedExtensions returns the file extensions this chunker handles.
+func (c *Chunker) SupportedExtensions() []string {
+	return []string{".ts", ".tsx", ".js", ".jsx"}
+}
+
+// Chunk parses a TypeScript/JavaScript source file and returns semantic code chunks.
+func (c *Chunker) Chunk(ctx context.Context, filePath string) ([]chunking.Chunk, error) {
+	// Read file content
+	content, err := os.ReadFile(filePath)
+	if err != nil {
+		return nil, fmt.Errorf("read file: %w", err)
+	}
+
+	// Parse the file
+	tree, err := c.parser.ParseCtx(ctx, nil, content)
+	if err != nil {
+		return nil, fmt.Errorf("parse TypeScript file: %w", err)
+	}
+	defer tree.Close()
+
+	sourceLines := strings.Split(string(content), "\n")
+	chunks := make([]chunking.Chunk, 0)
+
+	// Walk the AST and extract chunks
+	c.walkNode(tree.RootNode(), content, sourceLines, filePath, "", &chunks)
+
+	return chunks, nil
+}
+
+// walkNode recursively walks the tree-sitter AST and extracts chunks.
+func (c *Chunker) walkNode(node *sitter.Node, source []byte, sourceLines []string, filePath string, parentName string, chunks *[]chunking.Chunk) {
+	nodeType := node.Type()
+
+	switch nodeType {
+	case "function_declaration":
+		chunk := c.extractFunction(node, source, sourceLines, filePath, parentName)
+		if chunk != nil {
+			*chunks = append(*chunks, *chunk)
+		}
+
+	case "method_definition":
+		chunk := c.extractMethod(node, source, sourceLines, filePath, parentName)
+		if chunk != nil {
+			*chunks = append(*chunks, *chunk)
+		}
+
+	case "arrow_function", "function_expression":
+		// Handle arrow functions and function expressions assigned to variables
+		chunk := c.extractFunctionExpression(node, source, sourceLines, filePath, parentName)
+		if chunk != nil {
+			*chunks = append(*chunks, *chunk)
+		}
+
+	case "class_declaration":
+		chunk := c.extractClass(node, source, sourceLines, filePath)
+		if chunk != nil {
+			*chunks = append(*chunks, *chunk)
+
+			// Walk class body to find methods
+			for i := 0; i < int(node.ChildCount()); i++ {
+				child := node.Child(i)
+				if child.Type() == "class_body" {
+					c.walkNode(child, source, sourceLines, filePath, chunk.Name, chunks)
+				}
+			}
+		}
+		return // Don't walk children again
+
+	case "interface_declaration":
+		chunk := c.extractInterface(node, source, sourceLines, filePath)
+		if chunk != nil {
+			*chunks = append(*chunks, *chunk)
+		}
+
+	case "type_alias_declaration":
+		chunk := c.extractTypeAlias(node, source, sourceLines, filePath)
+		if chunk != nil {
+			*chunks = append(*chunks, *chunk)
+		}
+	}
+
+	// Walk all children
+	for i := 0; i < int(node.ChildCount()); i++ {
+		c.walkNode(node.Child(i), source, sourceLines, filePath, parentName, chunks)
+	}
+}
+
+// extractFunction extracts a function declaration.
+func (c *Chunker) extractFunction(node *sitter.Node, source []byte, sourceLines []string, filePath string, parentName string) *chunking.Chunk {
+	name := c.findChildContent(node, "identifier", source)
+	if name == "" {
+		return nil
+	}
+
+	startLine := int(node.StartPoint().Row) + 1
+	endLine := int(node.EndPoint().Row) + 1
+
+	chunk := &chunking.Chunk{
+		FilePath:   filePath,
+		Language:   chunking.LanguageTypeScript,
+		Type:       chunking.ChunkTypeFunction,
+		Name:       name,
+		ParentName: parentName,
+		StartLine:  startLine,
+		EndLine:    endLine,
+		Content:    c.extractLines(sourceLines, startLine, endLine),
+		Signature:  c.extractFunctionSignature(node, source, sourceLines),
+	}
+
+	// Extract JSDoc comment
+	if c.options.IncludeDocComments {
+		chunk.DocComment = c.extractComment(node, source)
+	}
+
+	return chunk
+}
+
+// extractMethod extracts a method definition from a class.
+func (c *Chunker) extractMethod(node *sitter.Node, source []byte, sourceLines []string, filePath string, parentName string) *chunking.Chunk {
+	name := c.findChildContent(node, "property_identifier", source)
+	if name == "" {
+		return nil
+	}
+
+	// Skip private methods if configured
+	if !c.options.IncludePrivate && strings.HasPrefix(name, "_") {
+		return nil
+	}
+
+	startLine := int(node.StartPoint().Row) + 1
+	endLine := int(node.EndPoint().Row) + 1
+
+	chunk := &chunking.Chunk{
+		FilePath:   filePath,
+		Language:   chunking.LanguageTypeScript,
+		Type:       chunking.ChunkTypeMethod,
+		Name:       name,
+		ParentName: parentName,
+		StartLine:  startLine,
+		EndLine:    endLine,
+		Content:    c.extractLines(sourceLines, startLine, endLine),
+		Signature:  c.extractMethodSignature(node, source, sourceLines),
+	}
+
+	// Extract JSDoc comment
+	if c.options.IncludeDocComments {
+		chunk.DocComment = c.extractComment(node, source)
+	}
+
+	return chunk
+}
+
+// extractFunctionExpression extracts arrow functions and function expressions.
+func (c *Chunker) extractFunctionExpression(node *sitter.Node, source []byte, sourceLines []string, filePath string, parentName string) *chunking.Chunk {
+	// Try to find the variable name from parent
+	parent := node.Parent()
+	if parent == nil {
+		return nil
+	}
+
+	var name string
+	if parent.Type() == "variable_declarator" {
+		name = c.findChildContent(parent, "identifier", source)
+	} else if parent.Type() == "assignment_expression" {
+		// Handle const foo = () => {}
+		for i := 0; i < int(parent.ChildCount()); i++ {
+			child := parent.Child(i)
+			if child.Type() == "identifier" || child.Type() == "member_expression" {
+				name = child.Content(source)
+				break
+			}
+		}
+	}
+
+	if name == "" {
+		return nil // Anonymous function, skip
+	}
+
+	startLine := int(node.StartPoint().Row) + 1
+	endLine := int(node.EndPoint().Row) + 1
+
+	chunk := &chunking.Chunk{
+		FilePath:   filePath,
+		Language:   chunking.LanguageTypeScript,
+		Type:       chunking.ChunkTypeFunction,
+		Name:       name,
+		ParentName: parentName,
+		StartLine:  startLine,
+		EndLine:    endLine,
+		Content:    c.extractLines(sourceLines, startLine, endLine),
+	}
+
+	return chunk
+}
+
+// extractClass extracts a class declaration.
+func (c *Chunker) extractClass(node *sitter.Node, source []byte, sourceLines []string, filePath string) *chunking.Chunk {
+	name := c.findChildContent(node, "type_identifier", source)
+	if name == "" {
+		return nil
+	}
+
+	startLine := int(node.StartPoint().Row) + 1
+	endLine := int(node.EndPoint().Row) + 1
+
+	chunk := &chunking.Chunk{
+		FilePath:  filePath,
+		Language:  chunking.LanguageTypeScript,
+		Type:      chunking.ChunkTypeClass,
+		Name:      name,
+		StartLine: startLine,
+		EndLine:   endLine,
+		Content:   c.extractLines(sourceLines, startLine, endLine),
+		Signature: c.extractClassSignature(node, source, sourceLines),
+	}
+
+	// Extract JSDoc comment
+	if c.options.IncludeDocComments {
+		chunk.DocComment = c.extractComment(node, source)
+	}
+
+	return chunk
+}
+
+// extractInterface extracts an interface declaration.
+func (c *Chunker) extractInterface(node *sitter.Node, source []byte, sourceLines []string, filePath string) *chunking.Chunk {
+	name := c.findChildContent(node, "type_identifier", source)
+	if name == "" {
+		return nil
+	}
+
+	startLine := int(node.StartPoint().Row) + 1
+	endLine := int(node.EndPoint().Row) + 1
+
+	chunk := &chunking.Chunk{
+		FilePath:  filePath,
+		Language:  chunking.LanguageTypeScript,
+		Type:      chunking.ChunkTypeInterface,
+		Name:      name,
+		StartLine: startLine,
+		EndLine:   endLine,
+		Content:   c.extractLines(sourceLines, startLine, endLine),
+	}
+
+	// Extract JSDoc comment
+	if c.options.IncludeDocComments {
+		chunk.DocComment = c.extractComment(node, source)
+	}
+
+	return chunk
+}
+
+// extractTypeAlias extracts a type alias declaration.
+func (c *Chunker) extractTypeAlias(node *sitter.Node, source []byte, sourceLines []string, filePath string) *chunking.Chunk {
+	name := c.findChildContent(node, "type_identifier", source)
+	if name == "" {
+		return nil
+	}
+
+	startLine := int(node.StartPoint().Row) + 1
+	endLine := int(node.EndPoint().Row) + 1
+
+	chunk := &chunking.Chunk{
+		FilePath:  filePath,
+		Language:  chunking.LanguageTypeScript,
+		Type:      chunking.ChunkTypeType,
+		Name:      name,
+		StartLine: startLine,
+		EndLine:   endLine,
+		Content:   c.extractLines(sourceLines, startLine, endLine),
+	}
+
+	return chunk
+}
+
+// findChildContent finds the first child of the given type and returns its content.
+func (c *Chunker) findChildContent(node *sitter.Node, childType string, source []byte) string {
+	for i := 0; i < int(node.ChildCount()); i++ {
+		child := node.Child(i)
+		if child.Type() == childType {
+			return child.Content(source)
+		}
+	}
+	return ""
+}
+
+// extractFunctionSignature extracts the function signature.
+func (c *Chunker) extractFunctionSignature(node *sitter.Node, source []byte, sourceLines []string) string {
+	startLine := int(node.StartPoint().Row) + 1
+
+	// Find the opening brace of the body
+	for i := 0; i < int(node.ChildCount()); i++ {
+		child := node.Child(i)
+		if child.Type() == "statement_block" {
+			endLine := int(child.StartPoint().Row) + 1
+			return strings.TrimSpace(c.extractLines(sourceLines, startLine, endLine-1))
+		}
+	}
+
+	// Fallback: just return first line
+	return strings.TrimSpace(c.extractLines(sourceLines, startLine, startLine))
+}
+
+// extractMethodSignature extracts the method signature.
+func (c *Chunker) extractMethodSignature(node *sitter.Node, source []byte, sourceLines []string) string {
+	startLine := int(node.StartPoint().Row) + 1
+
+	// Find the opening brace of the body
+	for i := 0; i < int(node.ChildCount()); i++ {
+		child := node.Child(i)
+		if child.Type() == "statement_block" {
+			endLine := int(child.StartPoint().Row) + 1
+			return strings.TrimSpace(c.extractLines(sourceLines, startLine, endLine-1))
+		}
+	}
+
+	return strings.TrimSpace(c.extractLines(sourceLines, startLine, startLine))
+}
+
+// extractClassSignature extracts the class declaration line.
+func (c *Chunker) extractClassSignature(node *sitter.Node, source []byte, sourceLines []string) string {
+	startLine := int(node.StartPoint().Row) + 1
+
+	// Find the opening brace of the class body
+	for i := 0; i < int(node.ChildCount()); i++ {
+		child := node.Child(i)
+		if child.Type() == "class_body" {
+			endLine := int(child.StartPoint().Row) + 1
+			return strings.TrimSpace(c.extractLines(sourceLines, startLine, endLine-1))
+		}
+	}
+
+	return strings.TrimSpace(c.extractLines(sourceLines, startLine, startLine))
+}
+
+// extractComment extracts JSDoc or other comments from a node.
+func (c *Chunker) extractComment(node *sitter.Node, source []byte) string {
+	// Check previous sibling for comment
+	prevSibling := node.PrevSibling()
+	if prevSibling != nil && prevSibling.Type() == "comment" {
+		comment := prevSibling.Content(source)
+		// Remove comment markers
+		comment = strings.TrimPrefix(comment, "/**")
+		comment = strings.TrimPrefix(comment, "/*")
+		comment = strings.TrimSuffix(comment, "*/")
+		comment = strings.TrimPrefix(comment, "//")
+		return strings.TrimSpace(comment)
+	}
+
+	return ""
+}
+
+// extractLines extracts a range of lines from source (1-indexed, inclusive).
+func (c *Chunker) extractLines(lines []string, start, end int) string {
+	if start < 1 || end < start || start > len(lines) {
+		return ""
+	}
+
+	startIdx := start - 1
+	endIdx := end
+	if endIdx > len(lines) {
+		endIdx = len(lines)
+	}
+
+	return strings.Join(lines[startIdx:endIdx], "\n")
+}