Fix: health-check reported success after reference search failed (#1998)

`project health-check` runs three tools but only two of them can fail the check: an
exception from `FindReferencingSymbolsTool` was caught and logged as a warning, while
the verdict tested `find_symbol_data` alone. The command therefore printed
"Health check passed - All tools working correctly" and exited 0 on a project whose
reference search had just blown up - the one signal a health check exists to give.

Co-authored-by: Arkadiusz Gładki <biosmoothly@gmail.com>

CHANGELOG.md

@@ -13,6 +13,12 @@ Status of the `main` branch. Changes prior to the next official version change w
     which could leave grandchildren as zombies; cleanup now waits for the discovered descendants (#1464)
   - Fix: `read_only` restriction in project definition was not applied to base tool set when in single-project context (#1938)
 
+* CLI:
+  - Fix: `project health-check` reported `Health check passed - All tools working correctly` and
+    exited 0 even when `FindReferencingSymbolsTool` had raised, because that failure was logged as
+    a warning while the verdict checked `FindSymbolTool` only. A reference-search failure now fails
+    the check; a symbol with no references is still a pass
+
 * Memories:
   - Fix: `save_memory`/`edit_memory` wrote directly to the memory file with `open(path, "w")`, which
     truncates it before the new content is written; a crash, OOM kill, or full disk partway through

src/serena/cli.py

@@ -1011,6 +1011,8 @@ class ProjectCommands(AutoRegisteringGroup):
                     )
                 find_symbol_data = json.loads(find_symbol_result)
                 log.info("FindSymbolTool found %d matches for symbol %s", len(find_symbol_data), symbol_name)
+                if not find_symbol_data:
+                    raise ProjectCommands._HealthCheckFailure("FindSymbolTool returned no results")
 
                 # Test 3: FindReferencingSymbolsTool
                 log.info("Testing FindReferencingSymbolsTool for symbol: %s", symbol_name)
@@ -1020,11 +1022,12 @@ class ProjectCommands(AutoRegisteringGroup):
                         find_refs_data = json.loads(find_refs_result)
                         log.info("FindReferencingSymbolsTool found %d references for symbol %s", len(find_refs_data), symbol_name)
                 except Exception as e:
-                    log.warning("FindReferencingSymbolsTool failed for symbol %s: %s", symbol_name, str(e))
-
-                # Verify tools worked as expected
-                if not find_symbol_data:
-                    raise ProjectCommands._HealthCheckFailure("FindSymbolTool returned no results")
+                    # A symbol with no references at all is a legitimate result, so the number of
+                    # references is not asserted - but a *failure* of the reference search means the
+                    # language server is not functional, which is the single thing this command is
+                    # asked to determine. Logging it as a warning let the command print
+                    # "All tools working correctly" and exit 0 after the search had already failed.
+                    raise ProjectCommands._HealthCheckFailure(f"FindReferencingSymbolsTool failed for symbol {symbol_name}: {e}") from e
 
                 log.info("Health check completed successfully")