general improvements (#17)

* refactor(hooks): simplify hook execution with shared context

- [x] Extract BaseInput struct to eliminate duplicate fields across hooks
- [x] Create RunHook handler pattern for session-start and user-prompt
- [x] Create RunStatuslineHook for fast statusline rendering without worker startup
- [x] Add HookContext struct to pass port, project, CWD, SessionID to handlers
- [x] Add db/interface.go with ObservationReader/Writer interfaces
- [x] Add comprehensive conflict management tests in sqlite/conflict_test.go
- [x] Add vector client tests for Count, ModelVersion, NeedsRebuild, GetStaleVectors
- [x] Add FilterByThreshold helper tests for query result filtering
- [x] Make handlers_test more robust for network-dependent update checks
- [x] Update package versions in UI

* Move to GORM + general cleanup

* feat(mcp): add observation relations discovery and scoring integration

- [x] Add find_related_observations MCP tool for discovering related observations by confidence
- [x] Integrate scoring calculator and recalculator into MCP server initialization
- [x] Add pattern, relation, and session stores to MCP server dependencies
- [x] Register MCP server in Claude Code settings during plugin installation
- [x] Update install scripts (bash, PowerShell) to configure MCP server settings
- [x] Switch plugin manifest files to template-based versioning (plugin.json.tpl, marketplace.json.tpl)
- [x] Update all MCP server tests to pass new dependency parameters

internal/mcp/server.go

@@ -9,7 +9,11 @@ import (
 	"io"
 	"os"
 
+	"github.com/lukaszraczylo/claude-mnemonic/internal/db/gorm"
+	"github.com/lukaszraczylo/claude-mnemonic/internal/scoring"
 	"github.com/lukaszraczylo/claude-mnemonic/internal/search"
+	"github.com/lukaszraczylo/claude-mnemonic/internal/vector/sqlitevec"
+	"github.com/lukaszraczylo/claude-mnemonic/pkg/models"
 	"github.com/rs/zerolog/log"
 )
 
@@ -19,15 +23,41 @@ type Server struct {
 	version   string
 	stdin     io.Reader
 	stdout    io.Writer
+
+	// Store dependencies for enhanced tools
+	observationStore *gorm.ObservationStore
+	patternStore     *gorm.PatternStore
+	relationStore    *gorm.RelationStore
+	sessionStore     *gorm.SessionStore
+	vectorClient     *sqlitevec.Client
+	scoreCalculator  *scoring.Calculator
+	recalculator     *scoring.Recalculator
 }
 
 // NewServer creates a new MCP server.
-func NewServer(searchMgr *search.Manager, version string) *Server {
+func NewServer(
+	searchMgr *search.Manager,
+	version string,
+	observationStore *gorm.ObservationStore,
+	patternStore *gorm.PatternStore,
+	relationStore *gorm.RelationStore,
+	sessionStore *gorm.SessionStore,
+	vectorClient *sqlitevec.Client,
+	scoreCalculator *scoring.Calculator,
+	recalculator *scoring.Recalculator,
+) *Server {
 	return &Server{
-		searchMgr: searchMgr,
-		version:   version,
-		stdin:     os.Stdin,
-		stdout:    os.Stdout,
+		searchMgr:        searchMgr,
+		version:          version,
+		stdin:            os.Stdin,
+		stdout:           os.Stdout,
+		observationStore: observationStore,
+		patternStore:     patternStore,
+		relationStore:    relationStore,
+		sessionStore:     sessionStore,
+		vectorClient:     vectorClient,
+		scoreCalculator:  scoreCalculator,
+		recalculator:     recalculator,
 	}
 }
 
@@ -333,6 +363,19 @@ func (s *Server) handleToolsList(req *Request) *Response {
 				},
 			},
 		},
+		{
+			Name:        "find_related_observations",
+			Description: "Find observations related to a given observation ID filtered by confidence threshold. Returns related observations sorted by confidence score. Useful for discovering relevant context.",
+			InputSchema: map[string]any{
+				"type":     "object",
+				"required": []string{"id"},
+				"properties": map[string]any{
+					"id":             map[string]any{"type": "number", "description": "Observation ID"},
+					"min_confidence": map[string]any{"type": "number", "default": 0.5, "minimum": 0.0, "maximum": 1.0, "description": "Minimum confidence threshold"},
+					"limit":          map[string]any{"type": "number", "default": 20, "minimum": 1, "maximum": 100},
+				},
+			},
+		},
 	}
 
 	return &Response{
@@ -388,6 +431,12 @@ func (s *Server) handleToolsCall(ctx context.Context, req *Request) *Response {
 
 // callTool dispatches to the appropriate tool handler.
 func (s *Server) callTool(ctx context.Context, name string, args json.RawMessage) (string, error) {
+	// Relation discovery tool
+	if name == "find_related_observations" {
+		return s.handleFindRelatedObservations(ctx, args)
+	}
+
+	// Original search-based tools
 	var params search.SearchParams
 	if err := json.Unmarshal(args, &params); err != nil {
 		return "", fmt.Errorf("invalid arguments: %w", err)
@@ -537,6 +586,72 @@ func (s *Server) handleTimelineByQuery(ctx context.Context, args json.RawMessage
 	return s.handleTimeline(ctx, args)
 }
 
+// handleFindRelatedObservations finds observations related to a given observation ID.
+func (s *Server) handleFindRelatedObservations(ctx context.Context, args json.RawMessage) (string, error) {
+	var params struct {
+		ID            int64   `json:"id"`
+		MinConfidence float64 `json:"min_confidence"`
+		Limit         int     `json:"limit"`
+	}
+	if err := json.Unmarshal(args, &params); err != nil {
+		return "", fmt.Errorf("invalid arguments: %w", err)
+	}
+
+	if params.ID == 0 {
+		return "", fmt.Errorf("id is required")
+	}
+
+	if params.MinConfidence == 0 {
+		params.MinConfidence = 0.5
+	}
+
+	if params.Limit == 0 {
+		params.Limit = 20
+	}
+	if params.Limit > 100 {
+		params.Limit = 100
+	}
+
+	// Get related observation IDs with confidence filter
+	relatedIDs, err := s.relationStore.GetRelatedObservationIDs(ctx, params.ID, params.MinConfidence)
+	if err != nil {
+		return "", fmt.Errorf("failed to get related observations: %w", err)
+	}
+
+	if relatedIDs == nil {
+		relatedIDs = []int64{}
+	}
+
+	// Limit results
+	if len(relatedIDs) > params.Limit {
+		relatedIDs = relatedIDs[:params.Limit]
+	}
+
+	// Fetch full observations
+	observations := make([]*models.Observation, 0, len(relatedIDs))
+	for _, id := range relatedIDs {
+		obs, err := s.observationStore.GetObservationByID(ctx, id)
+		if err != nil {
+			continue // Skip errors for individual observations
+		}
+		if obs != nil {
+			observations = append(observations, obs)
+		}
+	}
+
+	response := map[string]any{
+		"observations": observations,
+		"count":        len(observations),
+	}
+
+	output, err := json.Marshal(response)
+	if err != nil {
+		return "", fmt.Errorf("marshal response: %w", err)
+	}
+
+	return string(output), nil
+}
+
 // sendResponse sends a JSON-RPC response.
 func (s *Server) sendResponse(resp *Response) {
 	data, err := json.Marshal(resp)

internal/mcp/server_test.go

@@ -24,7 +24,7 @@ func TestServerSuite(t *testing.T) {
 
 // TestNewServer tests server creation.
 func (s *ServerSuite) TestNewServer() {
-	server := NewServer(nil, "1.0.0")
+	server := NewServer(nil, "1.0.0", nil, nil, nil, nil, nil, nil, nil)
 	s.NotNil(server)
 	s.Nil(server.searchMgr)
 	s.Equal("1.0.0", server.version)
@@ -293,7 +293,7 @@ func TestTimelineParams(t *testing.T) {
 
 // TestHandleInitialize tests the initialize handler.
 func TestHandleInitialize(t *testing.T) {
-	server := NewServer(nil, "1.2.3")
+	server := NewServer(nil, "1.2.3", nil, nil, nil, nil, nil, nil, nil)
 
 	req := &Request{
 		JSONRPC: "2.0",
@@ -320,7 +320,7 @@ func TestHandleInitialize(t *testing.T) {
 
 // TestHandleToolsList tests the tools/list handler.
 func TestHandleToolsList(t *testing.T) {
-	server := NewServer(nil, "1.0.0")
+	server := NewServer(nil, "1.0.0", nil, nil, nil, nil, nil, nil, nil)
 
 	req := &Request{
 		JSONRPC: "2.0",
@@ -361,7 +361,7 @@ func TestHandleToolsList(t *testing.T) {
 
 // TestHandleRequest tests request routing.
 func TestHandleRequest(t *testing.T) {
-	server := NewServer(nil, "1.0.0")
+	server := NewServer(nil, "1.0.0", nil, nil, nil, nil, nil, nil, nil)
 	ctx := context.Background()
 
 	tests := []struct {
@@ -423,7 +423,7 @@ func TestHandleRequest(t *testing.T) {
 
 // TestHandleToolsCall_InvalidParams tests tools/call with invalid params.
 func TestHandleToolsCall_InvalidParams(t *testing.T) {
-	server := NewServer(nil, "1.0.0")
+	server := NewServer(nil, "1.0.0", nil, nil, nil, nil, nil, nil, nil)
 	ctx := context.Background()
 
 	req := &Request{
@@ -442,7 +442,7 @@ func TestHandleToolsCall_InvalidParams(t *testing.T) {
 
 // TestCallTool_UnknownTool tests callTool with unknown tool name.
 func TestCallTool_UnknownTool(t *testing.T) {
-	server := NewServer(nil, "1.0.0")
+	server := NewServer(nil, "1.0.0", nil, nil, nil, nil, nil, nil, nil)
 	ctx := context.Background()
 
 	_, err := server.callTool(ctx, "nonexistent_tool", json.RawMessage(`{}`))
@@ -452,7 +452,7 @@ func TestCallTool_UnknownTool(t *testing.T) {
 
 // TestCallTool_InvalidArgs tests callTool with invalid arguments.
 func TestCallTool_InvalidArgs(t *testing.T) {
-	server := NewServer(nil, "1.0.0")
+	server := NewServer(nil, "1.0.0", nil, nil, nil, nil, nil, nil, nil)
 	ctx := context.Background()
 
 	_, err := server.callTool(ctx, "search", json.RawMessage(`invalid json`))
@@ -574,7 +574,7 @@ func TestJSONRPCErrorCodes(t *testing.T) {
 
 // TestToolListContainsExpectedSchemas tests that tool schemas are valid.
 func TestToolListContainsExpectedSchemas(t *testing.T) {
-	server := NewServer(nil, "1.0.0")
+	server := NewServer(nil, "1.0.0", nil, nil, nil, nil, nil, nil, nil)
 
 	req := &Request{
 		JSONRPC: "2.0",
@@ -600,7 +600,7 @@ func TestToolListContainsExpectedSchemas(t *testing.T) {
 
 // TestHandleToolsCall_UnknownTool tests tools/call with unknown tool name.
 func TestHandleToolsCall_UnknownTool(t *testing.T) {
-	server := NewServer(nil, "1.0.0")
+	server := NewServer(nil, "1.0.0", nil, nil, nil, nil, nil, nil, nil)
 	ctx := context.Background()
 
 	req := &Request{
@@ -620,7 +620,7 @@ func TestHandleToolsCall_UnknownTool(t *testing.T) {
 func TestCallTool_ToolNameRecognition(t *testing.T) {
 	// Note: This test verifies tool routing logic, not execution (which requires searchMgr)
 	// All valid tool names should be in the handleToolsList response
-	server := NewServer(nil, "1.0.0")
+	server := NewServer(nil, "1.0.0", nil, nil, nil, nil, nil, nil, nil)
 
 	req := &Request{
 		JSONRPC: "2.0",
@@ -782,7 +782,7 @@ func TestResponseIDTypes(t *testing.T) {
 
 // TestHandleTimelineByQuery_EmptyQuery tests timeline by query with empty query.
 func TestHandleTimelineByQuery_EmptyQuery(t *testing.T) {
-	server := NewServer(nil, "1.0.0")
+	server := NewServer(nil, "1.0.0", nil, nil, nil, nil, nil, nil, nil)
 	ctx := context.Background()
 
 	// Empty query should error
@@ -793,7 +793,7 @@ func TestHandleTimelineByQuery_EmptyQuery(t *testing.T) {
 
 // TestHandleTimeline_InvalidJSON tests timeline with invalid JSON.
 func TestHandleTimeline_InvalidJSON(t *testing.T) {
-	server := NewServer(nil, "1.0.0")
+	server := NewServer(nil, "1.0.0", nil, nil, nil, nil, nil, nil, nil)
 	ctx := context.Background()
 
 	_, err := server.handleTimeline(ctx, json.RawMessage(`{invalid`))
@@ -803,7 +803,7 @@ func TestHandleTimeline_InvalidJSON(t *testing.T) {
 
 // TestHandleTimelineByQuery_InvalidJSON tests timeline by query with invalid JSON.
 func TestHandleTimelineByQuery_InvalidJSON(t *testing.T) {
-	server := NewServer(nil, "1.0.0")
+	server := NewServer(nil, "1.0.0", nil, nil, nil, nil, nil, nil, nil)
 	ctx := context.Background()
 
 	_, err := server.handleTimelineByQuery(ctx, json.RawMessage(`{invalid`))
@@ -813,7 +813,7 @@ func TestHandleTimelineByQuery_InvalidJSON(t *testing.T) {
 
 // TestHandleTimeline_NoAnchorNoQuery tests timeline with no anchor and no query.
 func TestHandleTimeline_NoAnchorNoQuery(t *testing.T) {
-	server := NewServer(nil, "1.0.0")
+	server := NewServer(nil, "1.0.0", nil, nil, nil, nil, nil, nil, nil)
 	ctx := context.Background()
 
 	// No anchor_id and no query should return empty result
@@ -825,7 +825,7 @@ func TestHandleTimeline_NoAnchorNoQuery(t *testing.T) {
 
 // TestHandleTimeline_WithDefaults tests timeline default values are applied.
 func TestHandleTimeline_WithDefaults(t *testing.T) {
-	server := NewServer(nil, "1.0.0")
+	server := NewServer(nil, "1.0.0", nil, nil, nil, nil, nil, nil, nil)
 	ctx := context.Background()
 
 	// With anchor_id but no before/after, defaults should be applied
@@ -839,7 +839,7 @@ func TestHandleTimeline_WithDefaults(t *testing.T) {
 
 // TestServerFields tests Server struct fields.
 func TestServerFields(t *testing.T) {
-	server := NewServer(nil, "2.0.0")
+	server := NewServer(nil, "2.0.0", nil, nil, nil, nil, nil, nil, nil)
 
 	assert.Equal(t, "2.0.0", server.version)
 	assert.Nil(t, server.searchMgr)
@@ -891,7 +891,7 @@ func TestErrorWithNilData(t *testing.T) {
 
 // TestToolInputSchema tests that tool input schemas have required fields.
 func TestToolInputSchema(t *testing.T) {
-	server := NewServer(nil, "1.0.0")
+	server := NewServer(nil, "1.0.0", nil, nil, nil, nil, nil, nil, nil)
 
 	req := &Request{
 		JSONRPC: "2.0",
@@ -960,7 +960,7 @@ func TestToolCallParamsWithComplexArgs(t *testing.T) {
 
 // TestCallTool_UnknownToolName tests callTool with various unknown tool names.
 func TestCallTool_UnknownToolName(t *testing.T) {
-	server := NewServer(nil, "1.0.0")
+	server := NewServer(nil, "1.0.0", nil, nil, nil, nil, nil, nil, nil)
 	ctx := context.Background()
 
 	unknownTools := []string{
@@ -1009,7 +1009,7 @@ func TestTimelineParams_Validation(t *testing.T) {
 
 // TestHandleToolsCall_UnknownToolNameError tests tools/call with unknown tool returns error.
 func TestHandleToolsCall_UnknownToolNameError(t *testing.T) {
-	server := NewServer(nil, "1.0.0")
+	server := NewServer(nil, "1.0.0", nil, nil, nil, nil, nil, nil, nil)
 	ctx := context.Background()
 
 	req := &Request{
@@ -1031,7 +1031,7 @@ func TestHandleToolsCall_UnknownToolNameError(t *testing.T) {
 
 // TestHandleToolsCall_EmptyParams tests tools/call with empty params.
 func TestHandleToolsCall_EmptyParams(t *testing.T) {
-	server := NewServer(nil, "1.0.0")
+	server := NewServer(nil, "1.0.0", nil, nil, nil, nil, nil, nil, nil)
 	ctx := context.Background()
 
 	req := &Request{