Fixing documentation.

1. Corrected documentation to new structure in docker/plugins.yml file (from "repo" to "plugins").
2. To stick with USGS standards, migrated all .rst files in main directory to .md format, and made sphinx correctly process these.
3. Corrected links between files to be shown correctly.
4. Changed poetry install step to now use the newer install-poetry process.

Signed-off-by: Cliff Hill chill@contractor.usgs.gov