Move to Project Folders

[trisyoungs]

Currently we have an almost non-existent way of managing the data that Dissolve generates and the data which Dissolve requires, leading to a flat file structure which can be confusing to the users. This issue proposes to move to a project folder-style management, with Dissolve taking more responsibility in organising restart files / checkpoints, data output, and external data import.

This may look a little like:

MyProjectName/
├─ checkpoints/                # Restart points, one folder per point
│  ├─ equilibration/
│  │  ├─ checkpoint.restart
│  │  ├─ dangle.txt
│  ├─ first_test/
│  │  ├─ checkpoint.restart
│  ├─ refinement/
│  │  ├─ checkpoint.restart
├─ data/                        # Reference data, e.g. experimental data
│  ├─ NIMROD00095952.mint01
│  ├─ NIMROD00095953.mint01
│  ├─ xray.dat
├─ run/                         # Output from the current run
│  ├─ checkpoint.restart
│  ├─ dangle.txt
│  ├─ rdfbc.txt
├─ dissolve.dat                 # Project information
├─ input.txt                    # Main input file