claude_swarm 1.0.1 → 1.0.4

data/lib/swarm_memory/adapters/filesystem_adapter.rb

@@ -0,0 +1,845 @@
+# frozen_string_literal: true
+
+module SwarmMemory
+  module Adapters
+    # Real filesystem adapter using .md/.yml file pairs
+    #
+    # Architecture:
+    # - Content stored in .md files (markdown)
+    # - Metadata stored in .yml files (tags, confidence, hits)
+    # - Embeddings stored in .emb files (binary, optional)
+    # - Paths flattened with -- separator for Git-friendly structure
+    # - Stubs for merged/moved entries with auto-redirect
+    # - Hit tracking for access patterns
+    #
+    # Example on disk:
+    #   .swarm/memory/
+    #   ├── concepts--ruby--classes.md       (content)
+    #   ├── concepts--ruby--classes.yml      (metadata)
+    #   ├── concepts--ruby--classes.emb      (embedding, optional)
+    #   └── _stubs/
+    #       ├── old-ruby-intro.md            (stub: "# merged → concepts--ruby--classes")
+    #       └── old-ruby-intro.yml           (metadata with stub: true)
+    class FilesystemAdapter < Base
+      # Stub markers
+      STUB_MARKERS = ["# merged →", "# moved →"].freeze
+
+      # Virtual built-in entries that always exist without taking storage space
+      # These are meta-skills and resources available to all agents
+      # Mapped as: memory_path => gem_file_basename
+      VIRTUAL_ENTRIES = {
+        "skill/meta/deep-learning.md" => "meta/deep-learning",
+      }.freeze
+
+      # Initialize filesystem adapter with directory
+      #
+      # @param directory [String] Directory path for storage (REQUIRED)
+      # @raise [ArgumentError] If directory is not provided
+      def initialize(directory:)
+        super()
+        raise ArgumentError, "directory is required for FilesystemAdapter" if directory.nil? || directory.to_s.strip.empty?
+
+        @directory = File.expand_path(directory)
+        @semaphore = Async::Semaphore.new(1) # Fiber-aware concurrency control
+        @total_size = 0
+
+        # Create directory if it doesn't exist
+        FileUtils.mkdir_p(@directory)
+
+        # Lock file for cross-process synchronization
+        @lock_file_path = File.join(@directory, ".lock")
+
+        # Build in-memory index on boot (for fast lookups)
+        @index = build_index
+      end
+
+      # Write content to filesystem
+      #
+      # @param file_path [String] Logical path (e.g., "concepts/ruby/classes")
+      # @param content [String] Content to store
+      # @param title [String] Brief title
+      # @param embedding [Array<Float>, nil] Optional embedding vector
+      # @param metadata [Hash, nil] Optional metadata
+      # @return [Core::Entry] The created entry
+      def write(file_path:, content:, title:, embedding: nil, metadata: nil)
+        with_write_lock do
+          @semaphore.acquire do
+            raise ArgumentError, "file_path is required" if file_path.nil? || file_path.to_s.strip.empty?
+            raise ArgumentError, "content is required" if content.nil?
+            raise ArgumentError, "title is required" if title.nil? || title.to_s.strip.empty?
+
+            # Content is stored as-is (no frontmatter extraction)
+            # Metadata comes from tool parameters, not from content
+            content_size = content.bytesize
+
+            # Ensure all metadata keys are strings
+            stringified_metadata = metadata ? Utils.stringify_keys(metadata) : {}
+
+            # Check entry size limit
+            if content_size > MAX_ENTRY_SIZE
+              raise ArgumentError, "Content exceeds maximum size (#{format_bytes(MAX_ENTRY_SIZE)}). " \
+                "Current: #{format_bytes(content_size)}"
+            end
+
+            # Calculate new total size
+            existing_size = get_entry_size(file_path)
+            new_total_size = @total_size - existing_size + content_size
+
+            # Check total size limit
+            if new_total_size > MAX_TOTAL_SIZE
+              raise ArgumentError, "Memory storage full (#{format_bytes(MAX_TOTAL_SIZE)} limit). " \
+                "Current: #{format_bytes(@total_size)}, " \
+                "Would be: #{format_bytes(new_total_size)}. " \
+                "Clear old entries or use smaller content."
+            end
+
+            # Strip .md extension and flatten path for disk storage
+            # "concepts/ruby/classes.md" → "concepts--ruby--classes"
+            base_path = file_path.sub(/\.md\z/, "")
+            disk_path = flatten_path(base_path)
+
+            # 1. Write content to .md file (stored exactly as provided)
+            md_file = File.join(@directory, "#{disk_path}.md")
+            FileUtils.mkdir_p(File.dirname(md_file))
+            File.write(md_file, content)
+
+            # 2. Write metadata to .yml file
+            yaml_file = File.join(@directory, "#{disk_path}.yml")
+            existing_hits = read_yaml_field(yaml_file, :hits) || 0
+
+            yaml_data = {
+              title: title,
+              file_path: file_path, # Logical path with .md extension
+              updated_at: Time.now,
+              size: content_size,
+              hits: existing_hits, # Preserve hit count
+              metadata: stringified_metadata, # Metadata from tool parameters
+              embedding_checksum: embedding ? checksum(embedding) : nil,
+            }
+            # Convert symbol keys to strings for clean YAML output
+            File.write(yaml_file, YAML.dump(Utils.stringify_keys(yaml_data)))
+
+            # 3. Write embedding to .emb file (binary, optional)
+            if embedding
+              emb_file = File.join(@directory, "#{disk_path}.emb")
+              File.write(emb_file, embedding.pack("f*"))
+            end
+
+            # Update total size
+            @total_size = new_total_size
+
+            # Update index
+            @index[file_path] = {
+              disk_path: disk_path,
+              title: title,
+              size: content_size,
+              updated_at: Time.now,
+            }
+
+            # Return entry object
+            Core::Entry.new(
+              content: content,
+              title: title,
+              updated_at: Time.now,
+              size: content_size,
+              embedding: embedding,
+              metadata: stringified_metadata,
+            )
+          end
+        end
+      end
+
+      # Read content from filesystem
+      #
+      # @param file_path [String] Logical path with .md extension
+      # @return [String] Content
+      def read(file_path:)
+        raise ArgumentError, "file_path is required" if file_path.nil? || file_path.to_s.strip.empty?
+
+        # Check for virtual built-in entries first
+        if VIRTUAL_ENTRIES.key?(file_path)
+          entry = load_virtual_entry(file_path)
+          return entry.content
+        end
+
+        # Strip .md extension and flatten path
+        base_path = file_path.sub(/\.md\z/, "")
+        disk_path = flatten_path(base_path)
+        md_file = File.join(@directory, "#{disk_path}.md")
+
+        raise ArgumentError, "memory://#{file_path} not found" unless File.exist?(md_file)
+
+        content = File.read(md_file)
+
+        # Check if it's a stub (redirect)
+        if stub_content?(content)
+          target_path = extract_redirect_target(content)
+          return read(file_path: target_path) if target_path
+        end
+
+        # Increment hit counter
+        increment_hits(file_path)
+
+        content
+      end
+
+      # Read full entry with all metadata
+      #
+      # @param file_path [String] Logical path with .md extension
+      # @return [Core::Entry] Full entry object
+      def read_entry(file_path:)
+        raise ArgumentError, "file_path is required" if file_path.nil? || file_path.to_s.strip.empty?
+
+        # Check for virtual built-in entries first
+        if VIRTUAL_ENTRIES.key?(file_path)
+          return load_virtual_entry(file_path)
+        end
+
+        # Strip .md extension and flatten path
+        base_path = file_path.sub(/\.md\z/, "")
+        disk_path = flatten_path(base_path)
+        md_file = File.join(@directory, "#{disk_path}.md")
+        yaml_file = File.join(@directory, "#{disk_path}.yml")
+
+        raise ArgumentError, "memory://#{file_path} not found" unless File.exist?(md_file)
+
+        content = File.read(md_file)
+
+        # Follow stub redirect if applicable
+        if stub_content?(content)
+          target_path = extract_redirect_target(content)
+          return read_entry(file_path: target_path) if target_path
+        end
+
+        # Read metadata
+        yaml_data = File.exist?(yaml_file) ? YAML.load_file(yaml_file, permitted_classes: [Time, Date, Symbol]) : {}
+
+        # Read embedding if exists
+        emb_file = File.join(@directory, "#{disk_path}.emb")
+        embedding = if File.exist?(emb_file)
+          File.read(emb_file).unpack("f*")
+        end
+
+        # Increment hit counter
+        increment_hits(file_path)
+
+        Core::Entry.new(
+          content: content,
+          title: yaml_data["title"] || "Untitled",
+          updated_at: parse_time(yaml_data["updated_at"]) || Time.now,
+          size: yaml_data["size"] || content.bytesize,
+          embedding: embedding,
+          metadata: yaml_data["metadata"],
+        )
+      end
+
+      # Delete entry from filesystem
+      #
+      # @param file_path [String] Logical path with .md extension
+      # @return [void]
+      def delete(file_path:)
+        with_write_lock do
+          @semaphore.acquire do
+            raise ArgumentError, "file_path is required" if file_path.nil? || file_path.to_s.strip.empty?
+
+            # Strip .md extension and flatten path
+            base_path = file_path.sub(/\.md\z/, "")
+            disk_path = flatten_path(base_path)
+            md_file = File.join(@directory, "#{disk_path}.md")
+
+            raise ArgumentError, "memory://#{file_path} not found" unless File.exist?(md_file)
+
+            # Get size before deletion
+            entry_size = get_entry_size(file_path)
+
+            # Delete all related files
+            File.delete(md_file) if File.exist?(md_file)
+            File.delete(File.join(@directory, "#{disk_path}.yaml")) if File.exist?(File.join(@directory, "#{disk_path}.yaml"))
+            File.delete(File.join(@directory, "#{disk_path}.emb")) if File.exist?(File.join(@directory, "#{disk_path}.emb"))
+
+            # Update total size
+            @total_size -= entry_size
+
+            # Update index
+            @index.delete(file_path)
+          end
+        end
+      end
+
+      # List all entries
+      #
+      # @param prefix [String, nil] Filter by prefix
+      # @return [Array<Hash>] Entry metadata
+      def list(prefix: nil)
+        # Find all .md files (excluding stubs)
+        md_files = Dir.glob(File.join(@directory, "**/*.md"))
+          .reject { |f| stub_file?(f) }
+
+        entries = md_files.map do |md_file|
+          # Calculate logical path relative to @directory
+          logical_path = md_file.sub("#{@directory}/", "")
+          base_logical_path = logical_path.sub(/\.md\z/, "")
+
+          # Filter by prefix if provided (strip .md for comparison)
+          next if prefix && !base_logical_path.start_with?(prefix.sub(/\.md\z/, ""))
+
+          yaml_file = md_file.sub(".md", ".yml")
+          yaml_data = File.exist?(yaml_file) ? YAML.load_file(yaml_file, permitted_classes: [Time, Date, Symbol]) : {}
+
+          {
+            path: logical_path,
+            title: yaml_data["title"] || "Untitled",
+            size: yaml_data["size"] || File.size(md_file),
+            updated_at: parse_time(yaml_data["updated_at"]) || File.mtime(md_file),
+          }
+        end.compact
+
+        entries.sort_by { |e| e[:path] }
+      end
+
+      # Search by glob pattern
+      #
+      # @param pattern [String] Glob pattern (e.g., "concepts/**/*.md")
+      # @return [Array<Hash>] Matching entries
+      def glob(pattern:)
+        raise ArgumentError, "pattern is required" if pattern.nil? || pattern.to_s.strip.empty?
+
+        # Normalize pattern to ensure we only match .md files
+        # Standard glob behavior - just add .md extension intelligently
+        normalized_pattern = if pattern.end_with?("**")
+          # fact/** → fact/**/*.md (recursive match of all .md files)
+          "#{pattern}/*.md"
+        elsif pattern.end_with?("*")
+          # fact/* → fact/*.md (direct children .md files only)
+          "#{pattern}.md"
+        elsif pattern.end_with?(".md")
+          # Already has .md, use as-is
+          pattern
+        else
+          # No wildcard or extension, add .md
+          "#{pattern}.md"
+        end
+
+        # Use native Dir.glob with hierarchical paths - efficient!
+        glob_pattern = File.join(@directory, normalized_pattern)
+        md_files = Dir.glob(glob_pattern).reject { |f| stub_file?(f) }
+
+        results = md_files.map do |md_file|
+          # Calculate logical path relative to @directory
+          relative_path = md_file.sub("#{@directory}/", "")
+
+          yaml_file = md_file.sub(".md", ".yml")
+          yaml_data = File.exist?(yaml_file) ? YAML.load_file(yaml_file, permitted_classes: [Time, Date, Symbol]) : {}
+
+          {
+            path: relative_path,
+            title: yaml_data["title"] || "Untitled",
+            size: File.size(md_file),
+            updated_at: parse_time(yaml_data["updated_at"]) || File.mtime(md_file),
+          }
+        end
+
+        results.sort_by { |e| -e[:updated_at].to_f }
+      end
+
+      # Search by content pattern
+      #
+      # Fast path: grep .yml files first (metadata)
+      # Fallback: grep .md files (content)
+      #
+      # @param pattern [String] Regex pattern
+      # @param case_insensitive [Boolean] Case-insensitive search
+      # @param output_mode [String] Output mode
+      # @return [Array<Hash>] Results
+      def grep(pattern:, case_insensitive: false, output_mode: "files_with_matches", path: nil)
+        raise ArgumentError, "pattern is required" if pattern.nil? || pattern.to_s.strip.empty?
+
+        flags = case_insensitive ? Regexp::IGNORECASE : 0
+        regex = Regexp.new(pattern, flags)
+
+        case output_mode
+        when "files_with_matches"
+          grep_files_with_matches(regex, path)
+        when "content"
+          grep_with_content(regex, path)
+        when "count"
+          grep_with_count(regex, path)
+        else
+          raise ArgumentError, "Invalid output_mode: #{output_mode}"
+        end
+      end
+
+      # Clear all entries
+      #
+      # @return [void]
+      def clear
+        with_write_lock do
+          @semaphore.acquire do
+            # Delete all .md, .yml, .emb files
+            Dir.glob(File.join(@directory, "**/*.{md,yml,emb}")).each do |file|
+              File.delete(file)
+            end
+
+            @total_size = 0
+            @index = {}
+          end
+        end
+      end
+
+      # Get current total size
+      #
+      # @return [Integer] Total size in bytes
+      attr_reader :total_size
+
+      # Get number of entries
+      #
+      # @return [Integer] Number of entries
+      def size
+        @index.size
+      end
+
+      # Get all entries (for optimization/analysis)
+      #
+      # @return [Hash<String, Core::Entry>] All entries
+      def all_entries
+        entries = {}
+
+        @index.each do |logical_path, _index_data|
+          entries[logical_path] = read_entry(file_path: logical_path)
+        rescue ArgumentError
+          # Skip entries that can't be read
+          next
+        end
+
+        entries
+      end
+
+      # Semantic search by embedding vector
+      #
+      # Searches all entries with embeddings and returns those similar to the query.
+      # Results are sorted by cosine similarity in descending order.
+      #
+      # @param embedding [Array<Float>] Query embedding vector
+      # @param top_k [Integer] Number of results to return
+      # @param threshold [Float] Minimum similarity score (0.0-1.0)
+      # @return [Array<Hash>] Results with similarity scores
+      #
+      # @example
+      #   results = adapter.semantic_search(
+      #     embedding: query_embedding,
+      #     top_k: 5,
+      #     threshold: 0.65
+      #   )
+      def semantic_search(embedding:, top_k: 10, threshold: 0.0)
+        results = []
+
+        # Iterate all entries in the index
+        @index.each do |logical_path, index_data|
+          # Load embedding file
+          emb_file = File.join(@directory, "#{index_data[:disk_path]}.emb")
+          next unless File.exist?(emb_file)
+
+          # Read and unpack embedding
+          entry_embedding = File.read(emb_file).unpack("f*")
+
+          # Compute cosine similarity
+          similarity = cosine_similarity(embedding, entry_embedding)
+          next if similarity < threshold
+
+          # Load metadata from YAML
+          yaml_file = File.join(@directory, "#{index_data[:disk_path]}.yml")
+          yaml_data = if File.exist?(yaml_file)
+            YAML.load_file(yaml_file, permitted_classes: [Time, Date, Symbol])
+          else
+            {}
+          end
+
+          # Build result
+          results << {
+            path: logical_path,
+            similarity: similarity,
+            title: index_data[:title],
+            size: index_data[:size],
+            updated_at: index_data[:updated_at],
+            metadata: yaml_data["metadata"],
+          }
+        end
+
+        # Sort by similarity descending, return top K
+        results.sort_by { |r| -r[:similarity] }.take(top_k)
+      end
+
+      private
+
+      # Calculate cosine similarity between two vectors
+      #
+      # @param a [Array<Float>] First vector
+      # @param b [Array<Float>] Second vector
+      # @return [Float] Cosine similarity (0.0-1.0)
+      def cosine_similarity(a, b)
+        dot_product = a.zip(b).sum { |x, y| x * y }
+        magnitude_a = Math.sqrt(a.sum { |x| x**2 })
+        magnitude_b = Math.sqrt(b.sum { |x| x**2 })
+        dot_product / (magnitude_a * magnitude_b)
+      end
+
+      # Load virtual built-in entry from gem files
+      #
+      # Virtual entries are stored in lib/swarm_memory/skills/ as .md/.yml pairs
+      # and are always available without taking user storage space.
+      #
+      # @param file_path [String] Logical path (e.g., "skill/meta/deep-learning-protocol.md")
+      # @return [Core::Entry] Virtual entry object
+      def load_virtual_entry(file_path)
+        basename = VIRTUAL_ENTRIES[file_path]
+        skills_dir = File.expand_path("../skills", __dir__)
+
+        # Load content from .md file
+        md_file = File.join(skills_dir, "#{basename}.md")
+        content = File.read(md_file)
+
+        # Load metadata from .yml file
+        yml_file = File.join(skills_dir, "#{basename}.yml")
+        yaml_data = YAML.load_file(yml_file, permitted_classes: [Time, Date, Symbol])
+
+        Core::Entry.new(
+          content: content,
+          title: yaml_data["title"],
+          updated_at: Time.now,
+          size: content.bytesize,
+          embedding: nil,
+          metadata: yaml_data,
+        )
+      end
+
+      # Flatten path for disk storage
+      # "concepts/ruby/classes" → "concepts--ruby--classes"
+      #
+      # @param logical_path [String] Logical path with slashes
+      # @return [String] Flattened path with --
+      # Identity function - paths are now stored hierarchically
+      # Kept for backward compatibility during transition
+      #
+      # @param logical_path [String] Logical path
+      # @return [String] Same path (no flattening)
+      def flatten_path(logical_path)
+        logical_path
+      end
+
+      # Identity function - paths are now stored hierarchically
+      # Kept for backward compatibility during transition
+      #
+      # @param disk_path [String] Disk path
+      # @return [String] Same path (no unflattening)
+      def unflatten_path(disk_path)
+        disk_path
+      end
+
+      # Check if content is a stub (redirect)
+      #
+      # @param content [String] File content
+      # @return [Boolean] True if stub
+      def stub_content?(content)
+        STUB_MARKERS.any? { |marker| content.start_with?(marker) }
+      end
+
+      # Check if file is a stub
+      #
+      # @param file_path [String] Path to .md file
+      # @return [Boolean] True if stub
+      def stub_file?(file_path)
+        return false unless File.exist?(file_path)
+
+        # Read first 100 bytes to check for stub markers
+        content = File.read(file_path, 100)
+        stub_content?(content)
+      rescue StandardError
+        false
+      end
+
+      # Extract redirect target from stub content
+      #
+      # @param content [String] Stub content
+      # @return [String, nil] Target path or nil
+      def extract_redirect_target(content)
+        STUB_MARKERS.each do |marker|
+          next unless content.start_with?(marker)
+
+          # Extract path after marker
+          match = content.match(/#{Regexp.escape(marker)}\s+(.+?)$/m)
+          return match[1].strip if match
+        end
+        nil
+      end
+
+      # Increment hit counter for an entry
+      #
+      # @param file_path [String] Logical path with .md extension
+      # @return [void]
+      def increment_hits(file_path)
+        base_path = file_path.sub(/\.md\z/, "")
+        disk_path = flatten_path(base_path)
+        yaml_file = File.join(@directory, "#{disk_path}.yml")
+        return unless File.exist?(yaml_file)
+
+        @semaphore.acquire do
+          data = YAML.load_file(yaml_file, permitted_classes: [Time, Date, Symbol])
+          # Use string key to match the rest of the YAML file
+          data["hits"] = (data[:hits] || data["hits"] || 0) + 1
+          File.write(yaml_file, YAML.dump(data))
+        end
+      rescue StandardError => e
+        # Don't fail read if hit tracking fails
+        warn("Warning: Failed to increment hits for #{file_path}: #{e.message}")
+      end
+
+      # Get entry size from .yml or .md file
+      #
+      # @param file_path [String] Logical path with .md extension
+      # @return [Integer] Size in bytes
+      def get_entry_size(file_path)
+        base_path = file_path.sub(/\.md\z/, "")
+        disk_path = flatten_path(base_path)
+        yaml_file = File.join(@directory, "#{disk_path}.yml")
+
+        if File.exist?(yaml_file)
+          yaml_data = YAML.load_file(yaml_file, permitted_classes: [Time, Date, Symbol])
+          yaml_data["size"] || 0
+        else
+          md_file = File.join(@directory, "#{disk_path}.md")
+          File.exist?(md_file) ? File.size(md_file) : 0
+        end
+      rescue StandardError
+        0
+      end
+
+      # Read specific field from .yml file
+      #
+      # @param yaml_file [String] Path to .yml file
+      # @param field [Symbol, String] Field to read
+      # @return [Object, nil] Field value or nil
+      def read_yaml_field(yaml_file, field)
+        return unless File.exist?(yaml_file)
+
+        data = YAML.load_file(yaml_file, permitted_classes: [Time, Date, Symbol])
+        # YAML files always have string keys (we stringify when writing)
+        data[field.to_s]
+      rescue StandardError
+        nil
+      end
+
+      # Build in-memory index of all entries
+      #
+      # @return [Hash] Index mapping logical_path → metadata
+      def build_index
+        index = {}
+        total = 0
+
+        Dir.glob(File.join(@directory, "**/*.md")).each do |md_file|
+          next if stub_file?(md_file)
+
+          # Calculate logical path relative to @directory
+          logical_path = md_file.sub("#{@directory}/", "")
+          base_logical_path = logical_path.sub(/\.md\z/, "")
+
+          # disk_path is now the same as base_logical_path (no flattening)
+          disk_path = base_logical_path
+
+          yaml_file = md_file.sub(".md", ".yml")
+          yaml_data = File.exist?(yaml_file) ? YAML.load_file(yaml_file, permitted_classes: [Time, Date, Symbol]) : {}
+
+          size = yaml_data["size"] || File.size(md_file)
+          total += size
+
+          index[logical_path] = {
+            disk_path: disk_path,
+            title: yaml_data["title"] || "Untitled",
+            size: size,
+            updated_at: parse_time(yaml_data["updated_at"]) || File.mtime(md_file),
+          }
+        end
+
+        @total_size = total
+        index
+      end
+
+      # Grep for files with matches (fast path: .yml first)
+      #
+      # @param regex [Regexp] Pattern to match
+      # @return [Array<String>] Matching logical paths with .md extension
+      def grep_files_with_matches(regex, path_filter = nil)
+        results = []
+
+        # Fast path: Search .yml files (metadata)
+        Dir.glob(File.join(@directory, "**/*.yml")).each do |yaml_file|
+          next if yaml_file.include?("_stubs/")
+
+          # Calculate logical path relative to @directory
+          logical_path = yaml_file.sub("#{@directory}/", "").sub(".yml", ".md")
+          next unless matches_path_filter?(logical_path, path_filter)
+
+          content = File.read(yaml_file)
+          next unless regex.match?(content)
+
+          results << logical_path
+        end
+
+        # If found in metadata, return quickly
+        return results.sort unless results.empty?
+
+        # Fallback: Search .md files (content)
+        Dir.glob(File.join(@directory, "**/*.md")).each do |md_file|
+          next if stub_file?(md_file)
+
+          # Calculate logical path relative to @directory
+          logical_path = md_file.sub("#{@directory}/", "")
+          next unless matches_path_filter?(logical_path, path_filter)
+
+          content = File.read(md_file)
+          next unless regex.match?(content)
+
+          results << logical_path
+        end
+
+        results.uniq.sort
+      end
+
+      # Grep with content and line numbers
+      #
+      # @param regex [Regexp] Pattern to match
+      # @param path_filter [String, nil] Optional path prefix filter
+      # @return [Array<Hash>] Results with matches
+      def grep_with_content(regex, path_filter = nil)
+        results = []
+
+        Dir.glob(File.join(@directory, "**/*.md")).each do |md_file|
+          next if stub_file?(md_file)
+
+          # Calculate logical path relative to @directory
+          logical_path = md_file.sub("#{@directory}/", "")
+          next unless matches_path_filter?(logical_path, path_filter)
+
+          content = File.read(md_file)
+          matching_lines = []
+
+          content.each_line.with_index(1) do |line, line_num|
+            matching_lines << { line_number: line_num, content: line.chomp } if regex.match?(line)
+          end
+
+          next if matching_lines.empty?
+
+          results << {
+            path: logical_path,
+            matches: matching_lines,
+          }
+        end
+
+        results
+      end
+
+      # Grep with match counts
+      #
+      # @param regex [Regexp] Pattern to match
+      # @param path_filter [String, nil] Optional path prefix filter
+      # @return [Array<Hash>] Results with counts
+      def grep_with_count(regex, path_filter = nil)
+        results = []
+
+        Dir.glob(File.join(@directory, "**/*.md")).each do |md_file|
+          next if stub_file?(md_file)
+
+          # Calculate logical path relative to @directory
+          logical_path = md_file.sub("#{@directory}/", "")
+          next unless matches_path_filter?(logical_path, path_filter)
+
+          content = File.read(md_file)
+          count = content.scan(regex).size
+
+          next if count <= 0
+
+          results << {
+            path: logical_path,
+            count: count,
+          }
+        end
+
+        results
+      end
+
+      # Check if a logical path matches the filter
+      #
+      # Behaves like directory/file filtering even though paths are logical.
+      #
+      # @param logical_path [String] The logical path to check (e.g., "concept/ruby/blocks.md")
+      # @param path_filter [String, nil] Optional path prefix filter (e.g., "concept/", "fact/api-design", "skill/ruby/lambdas.md")
+      # @return [Boolean] True if path matches or no filter specified
+      #
+      # @example Directory-style filtering
+      #   matches_path_filter?("concept/ruby/blocks.md", "concept/") #=> true
+      #   matches_path_filter?("concept/ruby/blocks.md", "concept") #=> true
+      #   matches_path_filter?("fact/api-design/rest.md", "fact/api") #=> false (requires "fact/api/")
+      #   matches_path_filter?("fact/api/rest-basics.md", "fact/api") #=> true
+      #
+      # @example File-specific filtering
+      #   matches_path_filter?("concept/ruby/blocks.md", "concept/ruby/blocks.md") #=> true (exact match)
+      #   matches_path_filter?("concept/ruby/lambdas.md", "concept/ruby/blocks.md") #=> false
+      def matches_path_filter?(logical_path, path_filter)
+        return true if path_filter.nil? || path_filter.empty?
+
+        # If filter specifies a file (ends with .md), do exact match
+        return logical_path == path_filter if path_filter.end_with?(".md")
+
+        # Otherwise, treat as directory path
+        # Normalize: ensure filter ends with "/" for proper directory matching
+        # This prevents "fact/api" from matching "fact/api-design/"
+        dir_filter = path_filter.end_with?("/") ? path_filter : "#{path_filter}/"
+
+        logical_path.start_with?(dir_filter)
+      end
+
+      # Calculate checksum for embedding
+      #
+      # @param embedding [Array<Float>] Embedding vector
+      # @return [String] Hex checksum
+      def checksum(embedding)
+        Digest::MD5.hexdigest(embedding.pack("f*"))
+      end
+
+      # Parse time from various formats
+      #
+      # @param value [String, Time, nil] Time value
+      # @return [Time, nil] Parsed time
+      def parse_time(value)
+        return if value.nil?
+        return value if value.is_a?(Time)
+
+        Time.parse(value.to_s)
+      rescue ArgumentError
+        nil
+      end
+
+      # Execute block with cross-process write lock
+      #
+      # Uses flock to ensure exclusive access across processes.
+      # This prevents corruption when agent writes while defrag runs.
+      #
+      # @yield Block to execute with lock held
+      # @return [Object] Result of block
+      def with_write_lock
+        # Open lock file (create if doesn't exist)
+        File.open(@lock_file_path, File::RDWR | File::CREAT, 0o644) do |lock_file|
+          # Acquire exclusive lock (blocks if another process has it)
+          lock_file.flock(File::LOCK_EX)
+
+          begin
+            # Execute the block with lock held
+            yield
+          ensure
+            # Release lock
+            lock_file.flock(File::LOCK_UN)
+          end
+        end
+      end
+    end
+  end
+end