Store outputs and runtime metadata in separate files

[Artmann]

Move runtime metadata and execution outputs outside the primary notebook file to colocated .deepnoterun files. This provides stability similar to Marimo's .py files while maintaining rich environment context.

File Structure:

my-project.deepnote
.deepnote/
  ├── my-project.YYYYMMDDHHMMSSZ.deepnoterun  # Timestamped runs
  └── my-project.latestRun.deepnoterun        # Symlink or copy of latest

Benefits:

• Primary notebook only changes when code/structure changes (not on every execution)
• Better version control (cleaner diffs, less noise in git history)
• Preserve full execution history
• Rich environment context available for LLMs without polluting the main file

Related: deepnote/deepnote#160.