Enable Launch Protein Viewer from File(s) for terminal-opened/remote files

[Copilot]

Launch Protein Viewer from File(s) previously depended on Explorer context selection, so it could not reliably open files that were opened via integrated terminal workflows (including remote files outside watched workspace paths). This update makes command-palette invocation work against the active editor file when no Explorer selection is present.

• Command fallback behavior

  • Updated protein-viewer.activateFromFiles to resolve inputs in this order:
    1. selectedFiles (Explorer multi/single selection)
    2. file_uri (single URI invocation)
    3. vscode.window.activeTextEditor.document.uri (command-palette/terminal-opened file flow)
  • Shows a user-facing error when no resolvable file exists, instead of attempting to render with empty input.

• Documentation

  • Added README guidance for opening files from integrated terminal (including remote sessions) and then invoking Launch Protein Viewer from File(s) from the command palette.

• Code hygiene in touched path

  • Removed debug logging from the file activation command path.

const filesToOpen = selectedFiles && selectedFiles.length > 0
  ? selectedFiles
  : file_uri
    ? [file_uri]
    : vscode.window.activeTextEditor
      ? [vscode.window.activeTextEditor.document.uri]
      : [];

if (filesToOpen.length === 0) {
  void vscode.window.showErrorMessage("No structure file selected or active.");
  return;
}

ProteinViewerPanel.renderFromFiles(context.extensionUri, filesToOpen);