Rearrange cli commands

[masci]

This PR has no functional changes, it only rearrange the layout of the various command packages so that dependencies are cleaner, in particular:

1. cli package depends on all the packages implementing a command
2. None of the command packages depends on cli anymore
3. None of the root packages depends on cli anymore, except for main
4. output was removed from the root and added under cli since it's only used there

The new layout is this

cli
├── board
├── cli.go
├── cli_test.go
├── compile
├── config
├── core
├── daemon
├── errorcodes (to be used with os.Exit)
├── generatedocs
├── globals (for data that needs to be accessible to any command)
├── instance (common core operations used by different commands)
├── lib
├── output (common output operations, include contents of the old package at the root)
├── sketch
├── testdata
├── upload
└── version

PR also includes some minor changes to remove unneeded structs and indirection levels, as well as renaming few functions for clarity.

Tests were marked as Integration because they all interact with the actual repos. In the effort of keeping exported symbols at the bare minimum, some were un-exported but tests are now part of the same cli package, I think this use case is legit.