Fix bugs, implement requested enhancements

[gold2718]

This PR fixes some bugs and adds some new requested features:

• Speed up ice cataloging by using filename (with option to use data) Implement copy for non-NetCDF files
• Implement --compress-only which compresses but does not concatenate history files (Provide a no-concatenation option #7)
• Implement --keep-monthly which does not concatenate monthly history files when doing --yearly compression (Do not always concatenate all files #5)
• Improve error processing
• Update tests and add new regression tests
• Fix date retrieval from ocean files
• Add date range to --merge-all output files (Add time period to output file #4)
• Implemented a progress bar for file catalog step
• Improvements in error reporting
• Improvements in documentation (--help screen)
• Add compression or copying of restart files (using rest:rest component) (Include restart and / or initial data files? #3)

fixes #3
fixes #4
fixes #5
fixes #7

[gold2718]

@matsbn, To avoid having to review everything, please at least have a look at the new --compress-only option which compresses files (or just copies non-NetCDF files) but does no concatenation.
Note that for compress only, the default compression setting (2) does not seem to shrink the file size. However, setting --compress to a high number (e.g., 9) does shrink each file.

[gold2718]

@DirkOlivie, please have a look at the new --keep-monthly feature. Is this the expected behavior? Note that the monthly files so not seem to shrink (and sometimes grow a bit) with the default --compress setting of 2. Compression does seem to perform well using a higher setting such as 9.

[gold2718]

@lisesg,
Please have a look at the new --merge-all output filenames to verify that they are what you expect.

[lisesg]

Looks good!