Refactor to have references in separate sub-directory; closes #49

[dr-rodriguez]

This changes the database saving/loading logic to add an optional reference_database variable (defaults to "reference"). When set, any table set as reference will get stored in that sub-directory. This is backwards compatible in the sense that when loading a database, it will also check the parent directory if it doesn't file reference tables in the sub-directory.

Closes #49

[kelle]

This looks great! One question, do we really want reference/ to be a sub-directory of data/? This structure doesn't necessarily help with our navigation challenge.

SIMPLE-db/
├─ data/
│  ├─ 2mass source.json
│  ├─ asource.json
│  ├─ source1.json
│  ├─ reference_tables/
│  ├─ source2.json

Maybe we should we also have a sources sub-directory?

SIMPLE-db/
├─ data/
│  ├─ Sources/
│  │  ├─ 2mass source.json
│  │  ├─ source2.json
│  │  ├─ asource.json
│  │  ├─ source1.json
│  ├─ Reference_Tables/
│  │  ├─ Publications.json
│  │  ├─ Telescopes.json

Another option is to make the data/ and the reference/ directories both at the top level.

SIMPLE-db/
├─ data/
│  ├─ 2mass source.json
│  ├─ asource.json
│  ├─ source1.json
│  ├─ source2.json
├─ reference_tables/
│  ├─ Publications.json
│  ├─ Telescopes.json

[dr-rodriguez]

I do think they should be under data/ since both source data and references are data; having a separate top-level directory could lead to loosing part of the data.
Having a second sub-directory for the sources is something I thought about, but didn't try out. Seeing how relatively simple building this was I can probably do the same for the non-reference tables.

I can explore that over the next week. For ease of comparison I'll probably create a new branch off of this one, but we ideally want to merge both together.

So with that in place, we would have sources/ and references/ both under data/ which I thinkn is probably the cleanest setup. (We can iterate if those should be the best sub-directory names)

[dr-rodriguez]

This is now ready to go. It stores references under data/reference and sources under data/source. Tests are passing and I was able to create a PR for SIMPLE using this refactor at SIMPLE-AstroDB/SIMPLE-db#541

Once this is merged, I'll make a major astrodbkit2 release and re-run the SIMPLE tests.

[kelle]

Just added some suggested wording to the documentation. I've seen lots of folks struggle with paths and directory structure so I tried to make the structure more explicit throughout.