Clean up dev experience

[pdmnyberg]

This PR tries to clean up the dev environment in order to make it easier to get into the project.

It will:

• Update the README to reflect the current reality
• Add some utility .gitignore entries
• Remove unnecessary .DS_Store
• Make metabase optional in order to reduce complexity in dev scenarios
• Update the example data set in order to make it work out of the box

To test:

• Follow the README instructions
• Expect the system to start and load data without problems
• Try using the gitpod (I am not familiar with how to test this so feel free to suggest changes)

[pdmnyberg]

Would you mind having a look at this @mihai-sysbio maybe specifically the metabase related things.

[pdmnyberg]

This is a bit old now and can be done cleaner in another PR.