fix: get_symbol_detail returns source for branch/tag refs (Phase 0)

src/main/java/com/indexer/mcp/QueryExecutor.java

@@ -15,13 +15,10 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.IOException;
-import java.nio.file.Files;
 import java.nio.file.Path;
 import java.time.Instant;
 import java.util.*;
 import java.util.function.Supplier;
-import java.util.stream.Collectors;
 
 /**
  * Core query engine for the MCP server. All MCP tools delegate to this class.
@@ -241,7 +238,8 @@ public Map<String, Object> getSymbolDetail(String repo, String filePath, String
             sb.append("""
                     SELECT s.id, s.name, s.kind, s.signature, s.start_line, s.end_line,
                            s.parent_id, s.visibility, s.is_static,
-                           ef.path AS file_path, r.name AS repo_name, r.clone_path
+                           ef.id AS file_id,
+                           ef.path AS file_path, r.name AS repo_name
                     FROM symbols s
                     JOIN effective_files ef ON s.file_id = ef.id
                     JOIN repositories r ON ef.repo_id = r.id
@@ -277,10 +275,18 @@ public Map<String, Object> getSymbolDetail(String repo, String filePath, String
             int symbolId = ((Number) symbol.get("id")).intValue();
             int startLine = ((Number) symbol.get("start_line")).intValue();
             int endLine = ((Number) symbol.get("end_line")).intValue();
-            String clonePath = (String) symbol.get("clone_path");
+            long fileId = ((Number) symbol.get("file_id")).longValue();
 
-            // Read source lines from disk
-            symbol.put("source_code", readSourceLines(clonePath, filePath, startLine, endLine));
+            // Read source from the overlay-resolved file_contents row (ref-aware),
+            // not the on-disk working tree (which is always checked out to main).
+            String content = handle.createQuery(
+                            "SELECT content FROM file_contents WHERE file_id = :fileId")
+                    .bind("fileId", fileId)
+                    .mapTo(String.class)
+                    .findOne()
+                    .orElse(null);
+            symbol.put("source_code", sliceLines(content, startLine, endLine));
+            symbol.remove("file_id"); // internal id — not part of the response contract
 
             // Fetch children (e.g., methods if this is a class)
             var children = handle.createQuery("""
@@ -1649,22 +1655,24 @@ private void ensureBranchIndexed(String repo, String effectiveBranch) {
         }
     }
 
-    private String readSourceLines(String clonePath, String filePath, int startLine, int endLine) {
-        if (clonePath == null || clonePath.isBlank()) {
+    /**
+     * Slice lines [startLine, endLine] (1-based, inclusive) out of stored file content.
+     * Mirrors the old disk-based readSourceLines semantics but reads from file_contents
+     * (ref-aware via the effective_files overlay) instead of the working tree.
+     * Returns null when content is null (binary/oversized/metadata-only files).
+     */
+    private static String sliceLines(String content, int startLine, int endLine) {
+        if (content == null) {
             return null;
         }
-        try {
-            Path fullPath = Path.of(clonePath).resolve(filePath);
-            if (!Files.exists(fullPath)) {
-                return null;
-            }
-            List<String> lines = Files.readAllLines(fullPath);
-            int from = Math.max(0, startLine - 1);
-            int to = Math.min(lines.size(), endLine);
-            return lines.subList(from, to).stream().collect(Collectors.joining("\n"));
-        } catch (IOException e) {
-            log.warn("Could not read source lines from {}/{}: {}", clonePath, filePath, e.getMessage());
-            return null;
+        // String.lines() splits on \n, \r, and \r\n and drops a trailing terminator,
+        // matching Files.readAllLines — so symbol line numbers line up.
+        List<String> lines = content.lines().toList();
+        int from = Math.max(0, startLine - 1);
+        int to = Math.min(lines.size(), endLine);
+        if (from >= to) {
+            return "";
         }
+        return String.join("\n", lines.subList(from, to));
     }
 }

src/test/java/com/indexer/mcp/tools/BranchQueryTest.java

@@ -31,12 +31,13 @@ class BranchQueryTest {
     private int repoId;
     private FileDao fileDao;
     private SymbolDao symbolDao;
+    private Jdbi jdbi;
 
     @BeforeEach
     void setUp() {
         var dbManager = new DatabaseManager(postgres.getJdbcUrl(), postgres.getUsername(), postgres.getPassword());
         dbManager.initialize();
-        var jdbi = dbManager.getJdbi();
+        jdbi = dbManager.getJdbi();
         jdbi.useHandle(h -> {
             h.execute("DELETE FROM type_relationships");
             h.execute("DELETE FROM imports");
@@ -196,4 +197,65 @@ void getRepoSummaryCountsEffectiveFilesForBranch() {
         var branchSummary = queryExecutor.getRepoSummary("test-repo", "feature/new-auth");
         assertThat(((Number) branchSummary.get("fileCount")).intValue()).isEqualTo(2);
     }
+
+    @SuppressWarnings("unchecked")
+    @Test
+    void getSymbolDetailReturnsSourceForMainFile() {
+        int fileId = fileDao.upsert(new SourceFile(0, repoId, "main", "src/Detail.java", "java", 100, "abc", Instant.now()));
+        symbolDao.insertSymbol(new Symbol(0, fileId, "Detail", "class", "public class Detail", 2, 4, null, "public", false));
+        insertContent(fileId, "package x;\npublic class Detail {\n  int f;\n}\n");
+
+        var detail = queryExecutor.getSymbolDetail("test-repo", "src/Detail.java", "Detail", null, "main");
+
+        assertThat((String) detail.get("source_code")).isEqualTo("public class Detail {\n  int f;\n}");
+    }
+
+    @SuppressWarnings("unchecked")
+    @Test
+    void getSymbolDetailReturnsSourceForBranchOnlyFile() {
+        // File exists ONLY on the feature branch — the on-disk working tree (main) has no such file,
+        // so the old disk read returned null. This is the core bug.
+        int fileId = fileDao.upsert(new SourceFile(0, repoId, "feature/detail", "src/Only.java", "java", 100, "def", Instant.now()));
+        symbolDao.insertSymbol(new Symbol(0, fileId, "doThing", "method", "void doThing()", 1, 2, null, "public", false));
+        insertContent(fileId, "void doThing() {\n  return;\n}\n");
+
+        var detail = queryExecutor.getSymbolDetail("test-repo", "src/Only.java", "doThing", null, "feature/detail");
+
+        assertThat((String) detail.get("source_code")).isEqualTo("void doThing() {\n  return;");
+    }
+
+    @SuppressWarnings("unchecked")
+    @Test
+    void getSymbolDetailReturnsNullSourceForMetadataOnlyFile() {
+        // A file row + symbol but NO file_contents row (binary/oversized → content never stored).
+        int fileId = fileDao.upsert(new SourceFile(0, repoId, "main", "bin/Blob.bin", "binary", 999999, "abc", Instant.now()));
+        symbolDao.insertSymbol(new Symbol(0, fileId, "Blob", "class", "n/a", 1, 1, null, "public", false));
+        // intentionally no insertContent(...)
+
+        var detail = queryExecutor.getSymbolDetail("test-repo", "bin/Blob.bin", "Blob", null, "main");
+
+        assertThat(detail.get("source_code")).isNull();
+    }
+
+    @SuppressWarnings("unchecked")
+    @Test
+    void getSymbolDetailSlicesCorrectLineRange() {
+        int fileId = fileDao.upsert(new SourceFile(0, repoId, "main", "src/Slice.java", "java", 100, "abc", Instant.now()));
+        symbolDao.insertSymbol(new Symbol(0, fileId, "mid", "method", "void mid()", 3, 5, null, "public", false));
+        insertContent(fileId, "L1\nL2\nL3\nL4\nL5\nL6\n");
+
+        var detail = queryExecutor.getSymbolDetail("test-repo", "src/Slice.java", "mid", null, "main");
+
+        assertThat((String) detail.get("source_code")).isEqualTo("L3\nL4\nL5");
+    }
+
+    /** Insert (or replace) the stored content for a file. The DB trigger fills search_vector. */
+    private void insertContent(int fileId, String content) {
+        jdbi.useHandle(h -> h.createUpdate(
+                        "INSERT INTO file_contents (file_id, content) VALUES (:fid, :c) " +
+                                "ON CONFLICT (file_id) DO UPDATE SET content = EXCLUDED.content")
+                .bind("fid", fileId)
+                .bind("c", content)
+                .execute());
+    }
 }