Output file locations not always where you expect them to be

[conornally]

Some processes that produce outputs don't always put them where you expect.

If you give -Do DIR in bin/starbug2 then the resulting -ap file goes to DIR, however, a dither matched (123..)-ap catalogue gets exported into the current directory. --generate-region outputs in the current directory too. Regardless of input file location or -o output

There needs to be 1) uniform behaviour 2) a better-defined hierarchy of output options:

if given, -o output default input file directory probably never just in CWD

[conornally]

Most if not all outputs will now go to the correct folder. Plus the new OUTPUT parameter will allow you to set the basename for the output files. i.e -o folder/test.fits --> folder/test-ap.fits