Build/update 0.4.1

[mattyg]

• New holonix
• Update deps for holochain 0.4.1
• Pulled changes required to support holochain 0.4.1, latest profiles from branch Feat/p2p shipyard 0.4.x #270
• Cleanup very confusing npm scripts (still more confusing than I'd like)
• Bump version to 0.12.0

TODO

• Update holochain-prefix-index after this PR is merged Update to 0.4.1 and new holonix holochain-open-dev/holochain-prefix-index#12 and released
• Confirm all features working as expected
• Bump version

[mattyg]

Tests take an incredibly long time to run, and fill the log with error messages. I manually confirmed app features work as expected.

I opened another issue to investigate the test errors #274.

Going to merge this as is so I can get a release out.