Fix empty results when falling back to last completed run on PR path

- When auto-branch detects a PR and the current run is still in progress,
  the fallback path was using GetPRIssues which returns empty results
  because PR-level issues aren't populated until the run completes
- Switch to GetRunIssuesFlat with the fallback commit OID in this case,
  matching what the non-PR fallback path already does
- Add regression test for the PR fallback scenario (#6884175)

Author: jai-deepsource

command/issues/issues.go

@@ -349,7 +349,11 @@ func (opts *IssuesOptions) resolveIssues(ctx context.Context, client *deepsource
 		case ab.PRNumber > 0:
 			opts.PRNumber = ab.PRNumber
 			opts.CommitOid = ab.CommitOid
-			issuesList, err = client.GetPRIssues(ctx, remote.Owner, remote.RepoName, remote.VCSProvider, ab.PRNumber, prFilters)
+			if ab.Fallback {
+				issuesList, err = client.GetRunIssuesFlat(ctx, ab.CommitOid, serverFilters)
+			} else {
+				issuesList, err = client.GetPRIssues(ctx, remote.Owner, remote.RepoName, remote.VCSProvider, ab.PRNumber, prFilters)
+			}
 		case ab.UseRepo:
 			issuesList, err = client.GetIssues(ctx, remote.Owner, remote.RepoName, remote.VCSProvider)
 		default:

command/issues/tests/golden_files/get_analysis_runs_pr_fallback_completed_response.json

@@ -0,0 +1,46 @@
+{
+  "repository": {
+    "analysisRuns": {
+      "edges": [
+        {
+          "node": {
+            "runUid": "run-uid-running-01",
+            "commitOid": "831701c7a1b2c3d4e5f6a7b8c9d0e1f2a3b4c5d6",
+            "branchName": "feature/new-auth",
+            "status": "RUNNING",
+            "createdAt": "2025-03-12T14:00:00Z",
+            "finishedAt": null,
+            "updatedAt": "2025-03-12T14:01:00Z",
+            "summary": {
+              "occurrencesIntroduced": 0,
+              "occurrencesResolved": 0,
+              "occurrencesSuppressed": 0
+            },
+            "reportCard": null
+          }
+        },
+        {
+          "node": {
+            "runUid": "run-uid-completed-01",
+            "commitOid": "862df9f2e3a4b5c6d7e8f9a0b1c2d3e4f5a6b7c8",
+            "branchName": "feature/new-auth",
+            "status": "SUCCESS",
+            "createdAt": "2025-03-12T12:00:00Z",
+            "finishedAt": "2025-03-12T12:05:00Z",
+            "updatedAt": "2025-03-12T12:05:00Z",
+            "summary": {
+              "occurrencesIntroduced": 2,
+              "occurrencesResolved": 0,
+              "occurrencesSuppressed": 0
+            },
+            "reportCard": null
+          }
+        }
+      ],
+      "pageInfo": {
+        "hasNextPage": false,
+        "endCursor": null
+      }
+    }
+  }
+}

command/issues/tests/golden_files/get_analysis_runs_pr_fallback_first_response.json

@@ -0,0 +1,29 @@
+{
+  "repository": {
+    "analysisRuns": {
+      "edges": [
+        {
+          "node": {
+            "runUid": "run-uid-running-01",
+            "commitOid": "831701c7a1b2c3d4e5f6a7b8c9d0e1f2a3b4c5d6",
+            "branchName": "feature/new-auth",
+            "status": "RUNNING",
+            "createdAt": "2025-03-12T14:00:00Z",
+            "finishedAt": null,
+            "updatedAt": "2025-03-12T14:01:00Z",
+            "summary": {
+              "occurrencesIntroduced": 0,
+              "occurrencesResolved": 0,
+              "occurrencesSuppressed": 0
+            },
+            "reportCard": null
+          }
+        }
+      ],
+      "pageInfo": {
+        "hasNextPage": false,
+        "endCursor": null
+      }
+    }
+  }
+}

command/issues/tests/issues_test.go

@@ -420,6 +420,104 @@ func TestIssuesMultipleFilters(t *testing.T) {
 	}
 }
 
+// TestIssuesPRFallbackUsesRunIssues verifies that when auto-branch resolution
+// detects a PR AND the current run is in-progress (fallback), the code fetches
+// issues via GetRunIssuesFlat (commit-scoped) instead of GetPRIssues.
+// Regression test for ticket #6884175.
+func TestIssuesPRFallbackUsesRunIssues(t *testing.T) {
+	cfgMgr := testutil.CreateTestConfigManager(t, "test-token", "deepsource.com", "test@example.com")
+
+	// Load golden files for the multi-step mock.
+	prFoundData, err := os.ReadFile(goldenPath("get_pr_by_branch_found_response.json"))
+	if err != nil {
+		t.Fatalf("failed to read PR golden file: %v", err)
+	}
+	runsFirstData, err := os.ReadFile(goldenPath("get_analysis_runs_pr_fallback_first_response.json"))
+	if err != nil {
+		t.Fatalf("failed to read first runs golden file: %v", err)
+	}
+	runsCompletedData, err := os.ReadFile(goldenPath("get_analysis_runs_pr_fallback_completed_response.json"))
+	if err != nil {
+		t.Fatalf("failed to read completed runs golden file: %v", err)
+	}
+	commitScopeData, err := os.ReadFile(goldenPath("commit_scope_response.json"))
+	if err != nil {
+		t.Fatalf("failed to read commit scope golden file: %v", err)
+	}
+
+	mock := graphqlclient.NewMockClient()
+	analysisRunsCalls := 0
+	mock.QueryFunc = func(_ context.Context, query string, _ map[string]any, result any) error {
+		switch {
+		case strings.Contains(query, "pullRequests("):
+			return json.Unmarshal(prFoundData, result)
+		case strings.Contains(query, "query GetAnalysisRuns("):
+			analysisRunsCalls++
+			if analysisRunsCalls == 1 {
+				// First call (ResolveLatestRunForBranch, limit=1): RUNNING run
+				return json.Unmarshal(runsFirstData, result)
+			}
+			// Second call (ResolveLatestCompletedRun, limit=10): RUNNING + SUCCESS
+			return json.Unmarshal(runsCompletedData, result)
+		case strings.Contains(query, "checks {"):
+			// GetRunIssuesFlat for the fallback commit
+			return json.Unmarshal(commitScopeData, result)
+		default:
+			t.Fatalf("unexpected query: %s", query)
+			return nil
+		}
+	}
+	client := deepsource.NewWithGraphQLClient(mock)
+
+	var buf bytes.Buffer
+	deps := &cmddeps.Deps{
+		Client:    client,
+		ConfigMgr: cfgMgr,
+		Stdout:    &buf,
+		BranchNameFunc: func() (string, error) {
+			return "feature/new-auth", nil
+		},
+		HasUnpushedCommitsFunc:    func() bool { return false },
+		HasUncommittedChangesFunc: func() bool { return false },
+	}
+
+	cmd := issuesCmd.NewCmdIssuesWithDeps(deps)
+	cmd.SetArgs([]string{"--repo", "gh/testowner/testrepo", "--output", "json"})
+
+	if err := cmd.Execute(); err != nil {
+		t.Fatalf("unexpected error: %v", err)
+	}
+
+	got := buf.String()
+
+	// Verify the fallback info message is present.
+	if !strings.Contains(got, "Analysis is running on commit") {
+		t.Errorf("expected fallback info message, got: %q", got)
+	}
+
+	// Extract the JSON array from the output (after the info message line).
+	// The JSON starts at the first '[' character.
+	jsonStart := strings.Index(got, "[")
+	if jsonStart < 0 {
+		t.Fatalf("no JSON array found in output: %s", got)
+	}
+
+	var issues []map[string]any
+	if err := json.Unmarshal([]byte(got[jsonStart:]), &issues); err != nil {
+		t.Fatalf("failed to parse JSON output: %v\nraw output: %s", err, got)
+	}
+
+	// Must NOT be empty — this was the bug.
+	if len(issues) == 0 {
+		t.Fatal("expected non-empty issues from fallback commit, got empty array")
+	}
+
+	// Verify we got the expected issues from commit_scope_response.json.
+	if issues[0]["issue_code"] != "GO-W1007" {
+		t.Errorf("expected first issue GO-W1007, got %v", issues[0]["issue_code"])
+	}
+}
+
 func TestIssuesRunInProgress(t *testing.T) {
 	cfgMgr := testutil.CreateTestConfigManager(t, "test-token", "deepsource.com", "test@example.com")
 	mock := testutil.MockQueryFunc(t, map[string]string{