Merge remote-tracking branch 'origin/main' into codex/fix-issue1613-1703-1919

# Conflicts:
#	src/CodeIndex/Mcp/McpToolHandlers.cs
#	tests/CodeIndex.Tests/ConsoleUiTests.cs

Author: Widthdom

.github/workflows/dotnet.yml

@@ -182,7 +182,41 @@ jobs:
         run: dotnet build tests/CodeIndex.Tests/CodeIndex.Tests.csproj --configuration Release --framework ${{ matrix.test-framework }} --no-restore
 
       - name: Test
-        run: dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --configuration Release --framework ${{ matrix.test-framework }} --no-build --nologo --logger "trx;LogFileName=test_results.trx" --results-directory ./TestResults
+        shell: pwsh
+        run: |
+          $testArgs = @(
+            "test",
+            "tests/CodeIndex.Tests/CodeIndex.Tests.csproj",
+            "--configuration", "Release",
+            "--framework", "${{ matrix.test-framework }}",
+            "--no-build",
+            "--nologo",
+            "--settings", "tests/CodeIndex.Tests/CodeIndex.Tests.runsettings",
+            "--blame-crash",
+            "--blame-hang",
+            "--blame-hang-timeout", "5m",
+            "--logger", "trx;LogFileName=test_results.trx",
+            "--results-directory", "./TestResults"
+          )
+
+          dotnet @testArgs
+          $firstExitCode = $LASTEXITCODE
+          if ($firstExitCode -eq 0) {
+            exit 0
+          }
+
+          Write-Warning "Initial test run failed with exit code $firstExitCode. Rerunning once to classify possible flakiness."
+          dotnet @testArgs
+          $retryExitCode = $LASTEXITCODE
+          if ($retryExitCode -eq 0) {
+            New-Item -ItemType Directory -Force -Path ./TestResults | Out-Null
+            "Initial test run failed, but the single retry passed. Treat this run as flaky and inspect TRX/blame artifacts." |
+              Set-Content -Encoding UTF8 ./TestResults/flaky-retry.txt
+            Write-Warning "Tests passed on retry; uploaded TestResults include flaky-retry.txt."
+            exit 0
+          }
+
+          exit $retryExitCode
 
       - name: Summarize TRX telemetry
         if: always()
@@ -194,7 +228,14 @@ jobs:
         with:
           name: TestResults-${{ matrix.os }}-${{ matrix.test-framework }}
           if-no-files-found: warn
-          path: TestResults/**/*.trx
+          path: |
+            TestResults/**/*.trx
+            TestResults/**/*.txt
+            TestResults/**/*.xml
+            TestResults/**/*.dmp
+            TestResults/**/*.dump
+            TestResults/**/*Sequence*.xml
+            TestResults/**/*.hangdump
 
       - name: Publish
         if: matrix.os == 'ubuntu-latest' && matrix.test-framework == 'net8.0'

AGENT_GUIDE.md

@@ -131,7 +131,7 @@ CI watching must be bounded. Do not loop indefinitely.
 
 ## Status Contract
 
-- `status --json` and related JSON/MCP payloads currently expose the trust fields documented in `README.md` and `DEVELOPER_GUIDE.md`, including `fold_ready`, `fold_ready_reason`, `graph_table_available`, `issues_table_available`, `file_issues_data_current`, `migration_in_progress`, `sql_graph_contract_ready`, `sql_graph_contract_degraded_reason`, `hotspot_family_ready`, `hotspot_family_degraded_reason`, `csharp_symbol_name_ready`, `csharp_metadata_target_ready`, `csharp_metadata_target_degraded_reason`, `indexed_head_commit`, `worktree_head_changed`, `index_writer_version`, `index_newer_than_reader`, `index_newer_than_reader_reason`, `unknown_extension_file_count`, `path_case_sensitive`, `data_dir`, `data_dir_source`, `data_dir_mode`, `mac_profile`, `db_pragma_settings` (`journal_mode`, `synchronous`, `wal_autocheckpoint`, `page_count`, `freelist_count`, `page_size`), `hooks`, MCP-only `mcp_session`, and the `status --check`-only `stale_after_seconds` / `index_age_seconds` threshold audit fields.
+- `status --json` and related JSON/MCP payloads currently expose the trust fields documented in `README.md` and `DEVELOPER_GUIDE.md`, including `fold_ready`, `fold_ready_reason`, `graph_table_available`, `issues_table_available`, `file_issues_data_current`, `migration_in_progress`, `sql_graph_contract_ready`, `sql_graph_contract_degraded_reason`, `hotspot_family_ready`, `hotspot_family_degraded_reason`, `csharp_symbol_name_ready`, `csharp_metadata_target_ready`, `csharp_metadata_target_degraded_reason`, `indexed_head_commit`, `worktree_head_changed`, `index_writer_version`, `index_newer_than_reader`, `index_newer_than_reader_reason`, `unknown_extension_file_count`, `path_case_sensitive`, `data_dir`, `data_dir_source`, `data_dir_mode`, `mac_profile`, `db_size_bytes`, `wal_size_bytes`, `db_pragma_settings` (`journal_mode`, `synchronous`, `wal_autocheckpoint`, `page_count`, `freelist_count`, `page_size`), `symbols_by_language`, `process`, `last_index_run`, `hooks`, MCP-only `mcp_session`, and the `status --check`-only `stale_after_seconds` / `index_age_seconds` threshold audit fields.
 - When any readiness field is degraded, the CLI adds `degraded_root_cause`, `degraded_reason`, `recommended_action`, `alternative_action`, and `readiness_degradations[]`. `degraded_root_cause` is the primary stable machine code; `readiness_degradations[]` lists every degraded field with `root_cause`, human reason, and remediation strings.
 - `issues_table_available` reports physical `file_issues` table presence only. `file_issues_data_current` reports whether the table is also stamped current for the active index generation.
 - `index_writer_version` records the `cdidx` version that last wrote to the DB (stamped into `codeindex_meta` as `cdidx_writer_version` on every full scan, update, and MCP index). `index_newer_than_reader` flips to `true` whenever any persisted numeric contract stamp in `codeindex_meta` (or unknown `PRAGMA user_version` readiness bits) exceeds the current binary's compiled maximum, so an older CLI re-opening a DB written by a newer CLI degrades loudly with an audit trail instead of silently dropping back to text-search fallbacks. `index_newer_than_reader_reason` enumerates the specific newer-than-reader stamps.
@@ -140,6 +140,7 @@ CI watching must be bounded. Do not loop indefinitely.
 - `status` also surfaces `.cdidx` data-directory permissions via `data_dir_mode` on POSIX filesystems. New `.cdidx` data directories are forced to `0700`; the field is omitted on Windows, URI DBs, or when the directory mode cannot be inspected.
 - `status` also surfaces filesystem case-sensitivity via `path_case_sensitive`, stamped on every successful `cdidx index` run (full scan AND partial update, plus MCP-driven indexes) from `core.ignorecase` + a live filesystem probe. `true` means the volume is case-sensitive (`Foo.cs` and `foo.cs` are distinct); `false` means case-insensitive. Omitted on legacy DBs that predate the stamp. Use it to audit path-equality decisions on case-sensitive APFS, WSL NTFS / dev-drive, and ReFS mounts where the prior OS-keyed heuristic could mis-classify the workspace (#1546).
 - `status` also surfaces Linux mandatory-access-control context via `mac_profile` when `/proc/self/attr/current` or `/proc/self/attr/exec` indicates an AppArmor or SELinux profile. It is omitted on non-Linux hosts, unconstrained processes, or unreadable proc attributes (#1768).
+- `status` also surfaces DB/WAL size, per-language symbol-kind histograms, current process heap/GC/working-set metrics, and the last successful index run metadata. `process` is captured at status-call time; `last_index_run` is persisted at the end of successful CLI and MCP index runs and can include a peak-memory summary when CLI `--memory-trace` was used.
 - MCP `status` also surfaces session diagnostics via `mcp_session`. It is not persisted DB state; it includes the current `log_level`, captured `roots`, optional `client_info`, and optional `client_capabilities`.
 - Keep `README.md`, `DEVELOPER_GUIDE.md`, and this file synchronized if this contract changes.