Remove data bootstrapping; add folder reaping

- Entrypoint has new $PRE_RUNAS_CMD that allows running of root tasks before dropping privs.
- Added $SCITRAN_RUNTIME_PROTOCOL for explicit designation of http vs https.
- Updated README.md examples.
- No longer using requirements_dev.txt due to long install time.

Not happy with baking the pip requirement into the container. Need to think more.
Also, instructions in docker/README.md are broken.

Initialize Elasticsearch w/o connecting to Mongo

Retrofit of upload logic

closes #180

allow shallow hierarchy on /uploader

Group upsert

fixes #176

fix abort in base request handler
fix permissions when moving project

closes #175

closes #174

Bootstrap via http

Don't reference branches from within source. This allows core and testdata repo to move without breaking not up-to-date versions of core. Also allows branches to be fully merged.

Still a similar branch reference in bin/run.sh

Now supports API enabled bootstrapping.

requires #171