Refactor Github documentation

**Describe the task**
Documentation for our development setup is unstructured and lacks context. This results in confusion and wasted time. Refactor the documentation, have it reviewed by the team for agreed upon clarity.

**Acceptance Criteria**
- [ ] Break up API README into linked markdown files for OS setup, R, setup, Python setup, Java setup, database setup, cluster/operational setup, so that the different pieces of the stack are self contained
- [ ] Remove any conflicting statements around setups
- [ ] Include any missing context (missing GDAL commands, missing context around R env usage)
- [ ] Include machine version and dependency versions that the install steps work with
- [ ] Script more parts of the setup that can be automated and remove the documentation that it replaces.

**Additional context**
- This may need to be broken up into separate tickets.

Locate the API README and review its current setup sections for OS, R, Python, Java, database, and cluster or operational setup. Identify conflicting or missing context, including GDAL commands and R environment usage, then define the linked documentation and automation changes needed to satisfy the acceptance criteria and obtain team review.

Written by the indexing model from the issue text.