Enhancements to directory handling

• Changed the handling of paths to make them relative to the directory that the step is running in. In a loop, for instance, files are relative to the iteration directory.
• When reading files, allow the syntax 'job:///...' to read files from another job. If the job number is omitted, so the prefix is 'job:///...', the top directory of the current job is used.

Added new names for systems and configurations

• Made the naming of systems and configurations consistent with the standard parameters for them in the GUI.
• Removed all "from file" options, replacing them with "title", which means the title from the file, if it exists, or the filename if it doesn't.

Bugfix: Crash due to multiple slashes in titles in SDF files

Merge pull request #51 from molssi-seamm/dev

Fixed crash due to multiple slashes in titles.

Added writers for CIF and mmCIF.

Merge pull request #50 from molssi-seamm/dev

Added writers for CIF and mmCIF.

Initial changes to structure handling

Moving towards the standard structure handling that has developed across SEAMM.

Add support for bonds in CIF files

Now correctly handle spacegroup symmetry and bonds in CIF files.

Added ability to select ranges of structures for XYZ and SDF files

Merge pull request #47 from molssi-seamm/dev

Fixed selection of ranges

Removed debug printing left accidentally

Merge pull request #46 from molssi-seamm/dev

Removed debug printing

Support for .gz and .bz2 files, and multi-structure .xyz files

• Handle .gz and .bz2 files for .sdf and .xyz extensions.
• Handle multi-structure XYZ files with a blank line between records.

Bugfixes: improved output writing files.

• Fixed output of number of structures written to SDF files, which was off by 1.
• Cleaned up the output for the write-structure step