fix(analyzer): defensive skip when second_pass references untracked file

In source_analyzer.second_pass, the list of files we iterate can include
paths that first_pass did not add to self.files (e.g. parse errors,
LSP-induced timeouts, or rare edge cases where a candidate file is
present in the input list but never makes it into the files map).
Previously this raised KeyError and aborted the entire index. Hit on
sympy/polys/distributedmodules.py during bench calibration of sympy-12481.

Skip with a WARN log instead so a single bad file no longer takes down
the whole index.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Author: DvirDukhan

api/analyzers/source_analyzer.py

@@ -180,7 +180,16 @@ def second_pass(self, graph: Graph, files: list[Path], path: Path) -> None:
                 # Skip symbol resolution when no real LSP is available
                 if isinstance(lsps.get(file_path.suffix), NullLanguageServer):
                     continue
-                file = self.files[file_path]
+                file = self.files.get(file_path)
+                if file is None:
+                    # first_pass skipped this file (e.g. parse error, empty,
+                    # or ignored after entering the candidate list). Skip
+                    # in second_pass too instead of crashing the whole index.
+                    logging.warning(
+                        "second_pass: %s not in files map (first_pass skipped it); skipping",
+                        file_path,
+                    )
+                    continue
                 logging.info(f'Processing file ({i + 1}/{files_len}): {file_path}')
                 for _, entity in file.entities.items():
                     entity.resolved_symbol(lambda key, symbol, fp=file_path: analyzers[fp.suffix].resolve_symbol(self.files, lsps[fp.suffix], fp, path, key, symbol))