Popup

[dprada]

This pull request brings several documentation updates and improvements for developer and contributor workflows, clarifies the architecture and synchronization mechanisms between Python and TypeScript layers, and adds checkpoint documentation for new features. The changes focus on making the development process clearer, improving onboarding, and documenting the implementation status of regions/layers and the new popup feature.

Developer workflow and repository structure:

• Updated documentation to clarify that the JavaScript bundle (molsysviewer/viewer.js) is now tracked in the repository so users do not need a Node/TypeScript toolchain, and provided more precise instructions for rebuilding and updating checkpoints. [1] [2]
• Fixed and standardized paths for conda environment files and directories, and updated Python file references for clarity. [1] [2] [3] [4] [5] [6]

Contribution and build artifact guidance:

• Improved contributor guidelines to specify the correct TypeScript source directory and clarified the build artifact workflow.
• Added explicit instructions in AGENTS.md to not read or edit generated files (viewer.js, viewer.js.map), emphasizing that only TypeScript sources should be referenced for logic changes.

Architecture and implementation documentation:

• Added a comprehensive architecture document detailing the Python↔TypeScript message protocol, data flows, visibility handling, regions/layers API, and the new popup synchronization mechanism.
• Updated checkpoint documentation for regions/layers to reflect that the messaging schema and acknowledgment path are now implemented, and clarified the current status and pending improvements.
• Added a new checkpoint document describing the popup ("popout") feature: its objectives, current implementation, synchronization details, limitations, and next steps.