Change reconstruction outputs to single file.

[Linked-Liszt]

Currently the reconstruction program outputs multiple individual files, one for each frame. This is a inefficient way of doing things, It's rough on the filesystem especially as a single scan can produce many thousands of files.

This will require

• Modifying the C and CUDA implementations to write out to a single file. Might need to change memory management too to support that, especially in a multiprocessing setting.
• Modifying the peaksearch program to read through read an individual file. Jon suggested keeping the single-layer processing capability and to pass in an index as an additional parameter to keep process-level parallelization. A more robust solution would involve passing in a range but would be a significantly larger refactor.