fix(indexer): suppress conflicting Go package aliases

Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)

Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>

Author: tae2089

internal/service/indexer.go

@@ -1,11 +1,11 @@
 package service
 
 import (
+	"bufio"
 	"context"
 	"crypto/sha256"
 	"encoding/gob"
 	"encoding/hex"
-	"bufio"
 	"errors"
 	"fmt"
 	"log/slog"
@@ -85,7 +85,7 @@ type updateSpool struct {
 
 var (
 	testBuildBatchReleaseHook func([]parsedBuildNodeBatch, int)
-	resolveBuildEdges          = edgeresolve.Resolve
+	resolveBuildEdges         = edgeresolve.Resolve
 )
 
 const (
@@ -1294,6 +1294,7 @@ func collectGoImportPackages(absDir string, opts BuildOptions, parserForExt func
 		return nil, err
 	}
 	packages := make(map[string]string)
+	ambiguous := make(map[string]struct{})
 	err = walkMatchingFiles(context.Background(), absDir, opts, func(path, relPath string) error {
 		if strings.ToLower(filepath.Ext(path)) != ".go" {
 			return nil
@@ -1312,11 +1313,13 @@ func collectGoImportPackages(absDir string, opts BuildOptions, parserForExt func
 			return nil
 		}
 		dir := filepath.ToSlash(filepath.Dir(relPath))
+		importPath := modulePath
 		if dir == "." {
-			packages[modulePath] = pkgName
+			rememberGoImportPackage(packages, ambiguous, importPath, pkgName)
 			return nil
 		}
-		packages[modulePath+"/"+dir] = pkgName
+		importPath = modulePath + "/" + dir
+		rememberGoImportPackage(packages, ambiguous, importPath, pkgName)
 		return nil
 	})
 	if err != nil {
@@ -1325,6 +1328,19 @@ func collectGoImportPackages(absDir string, opts BuildOptions, parserForExt func
 	return packages, nil
 }
 
+
+func rememberGoImportPackage(packages map[string]string, ambiguous map[string]struct{}, importPath, pkgName string) {
+	if _, blocked := ambiguous[importPath]; blocked {
+		return
+	}
+	if existing, ok := packages[importPath]; ok && existing != pkgName {
+		delete(packages, importPath)
+		ambiguous[importPath] = struct{}{}
+		return
+	}
+	packages[importPath] = pkgName
+}
+
 func readGoModulePath(goModPath string) (string, error) {
 	file, err := os.Open(goModPath)
 	if err != nil {

internal/service/indexer_test.go

@@ -82,10 +82,10 @@ func countServiceSQLInList(sql string) int {
 }
 
 type recordingGraphStore struct {
-	t         *testing.T
-	ops       []string
-	nextID    uint
-	nodesByFP map[string][]model.Node
+	t             *testing.T
+	ops           []string
+	nextID        uint
+	nodesByFP     map[string][]model.Node
 	edges         []model.Edge
 	upsertedEdges [][]model.Edge
 }
@@ -604,6 +604,64 @@ func TestBuild_UsesRepoLocalPackageClauseForGoImportAssertions(t *testing.T) {
 	t.Fatalf("expected implements edge from %d to contracts.Service %d, got %+v", impl.ID, iface.ID, edges)
 }
 
+func TestBuild_SuppressesRepoLocalPackageClauseCorrectionOnConflict(t *testing.T) {
+	db, err := gorm.Open(sqlite.Open(":memory:"), &gorm.Config{Logger: gormlogger.Discard})
+	if err != nil {
+		t.Fatalf("open db: %v", err)
+	}
+	st := gormstore.New(db)
+	if err := st.AutoMigrate(); err != nil {
+		t.Fatalf("migrate: %v", err)
+	}
+
+	svc := &GraphService{Store: st, DB: db, Walkers: map[string]*treesitter.Walker{".go": treesitter.NewWalker(treesitter.GoSpec)}, Logger: slog.Default()}
+
+	tmpDir := t.TempDir()
+	mustMkdir := func(rel string) {
+		if err := os.MkdirAll(filepath.Join(tmpDir, rel), 0o755); err != nil {
+			t.Fatalf("mkdir %s: %v", rel, err)
+		}
+	}
+	mustWrite := func(rel, content string) {
+		if err := os.WriteFile(filepath.Join(tmpDir, rel), []byte(content), 0o644); err != nil {
+			t.Fatalf("write %s: %v", rel, err)
+		}
+	}
+	mustWrite("go.mod", "module github.com/example/project\n\ngo 1.25.0\n")
+	mustMkdir("internal/api")
+	mustMkdir("mainpkg")
+	mustWrite("internal/api/a.go", "package contracts\n\ntype Service interface {\n\tRun()\n}\n")
+	mustWrite("internal/api/b.go", "package other\n\ntype Service interface {\n\tRun()\n}\n")
+	mustWrite("mainpkg/main.go", "package mainpkg\n\nimport dep \"github.com/example/project/internal/api\"\n\ntype MyType struct{}\n\nfunc (MyType) Run() {}\n\nvar _ dep.Service = MyType{}\n")
+
+	ctx := context.Background()
+	if _, err := svc.Build(ctx, BuildOptions{Dir: tmpDir}); err != nil {
+		t.Fatalf("Build: %v", err)
+	}
+
+	impl, err := st.GetNode(ctx, "mainpkg.MyType")
+	if err != nil || impl == nil {
+		t.Fatalf("GetNode impl: node=%v err=%v", impl, err)
+	}
+	iface, err := st.GetNode(ctx, "contracts.Service")
+	if err != nil || iface == nil {
+		t.Fatalf("GetNode iface: node=%v err=%v", iface, err)
+	}
+	otherIface, err := st.GetNode(ctx, "other.Service")
+	if err != nil || otherIface == nil {
+		t.Fatalf("GetNode other iface: node=%v err=%v", otherIface, err)
+	}
+	edges, err := st.GetEdgesFrom(ctx, impl.ID)
+	if err != nil {
+		t.Fatalf("GetEdgesFrom: %v", err)
+	}
+	for _, edge := range edges {
+		if edge.Kind == model.EdgeKindImplements && (edge.ToNodeID == iface.ID || edge.ToNodeID == otherIface.ID) {
+			t.Fatalf("expected conflicting package clauses to suppress alias correction, got implements edge %+v", edge)
+		}
+	}
+}
+
 func TestNewParsedBuildNodeBatch_DropsRawContentAndOnlyBuildsSourceLinesWhenNeeded(t *testing.T) {
 	typ := reflect.TypeFor[parsedBuildNodeBatch]()
 	if _, ok := typ.FieldByName("content"); ok {