Cleanup unnecessary abstractions in integration-cli

There were several unnecessary abstractions integration-cli:

- `startCommand`
- `nLines`
- `deepEqual`

We only used them in one or two tests and forget about them when adding new ones, so we may as well just get rid of them all together.

BONUS: found that the libtrust path was imported inconsistently and fixed that too. I can put that one in another PR but it seemed easier like this. LMK.