fix(analyzers): guard against KeyError for ignored files in second_pass

Files skipped by first_pass() via the ignore list are not added to
self.files, but second_pass() iterated the same files list and
dereferenced self.files[file_path] unconditionally. This would raise
KeyError for any ignored file.

Add a membership check before accessing self.files and reorder the
guards so both the membership check and NullLanguageServer skip happen
before dereferencing.

Addresses review comment: coderabbitai suggested adding a guard to
skip files not in self.files before indexing.

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

Author: gkorland

api/analyzers/source_analyzer.py

@@ -149,11 +149,13 @@ def second_pass(self, graph: Graph, files: list[Path], path: Path) -> None:
         with lsps[".java"].start_server(), lsps[".py"].start_server(), lsps[".cs"].start_server(), lsps[".js"].start_server():
             files_len = len(self.files)
             for i, file_path in enumerate(files):
-                file = self.files[file_path]
-                logging.info(f'Processing file ({i + 1}/{files_len}): {file_path}')
+                if file_path not in self.files:
+                    continue
                 # Skip symbol resolution when no real LSP is available
                 if isinstance(lsps.get(file_path.suffix), NullLanguageServer):
                     continue
+                file = self.files[file_path]
+                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))
                     for key, symbols in entity.symbols.items():