Tolerating deletion of projects within CS as well as their folders in the file system
Add new protocols:
* **3D Flex Data Prep**: Prepares particles for use in 3DFlex training and reconstruction. At the same way, Takes in a consensus (rigid) refinement density map, plus optionally a segmentation and generates a tetrahedral mesh for 3DFlex.
* **3D Flex Mesh Prep**: Takes in a consensus (rigid) refinement density map, plus optionally a segmentation and generates a tetrahedral mesh for 3DFlex. See Mesh Generation below.
* **3D Flex Training**: Uses a mesh and prepared particles (at a downsampled resolution) to train a 3DFlex model. Parameters control the number of latent dimensions, size of the model, and training hyperparameters. This job outputs checkpoints during training.
* **3D Flex Reconstruction**: Takes in a checkpoint from training as well as prepared high-resolution particles and performs high-resolution refinement using L-BFGS under the 3DFlex model. This is the stage at which improvements to density in high-res regions are computed. Outputs two half-maps that can be used for FSC validation, sharpening, and other downstream tasks.
Allowing Scipion to import coordinates