Remove some subjective extensions, add .gitignore

[ewels]

I find myself routinely disabling some extensions that we have in the extension pack, the indentation colouration primarily.

I think that we should keep the extension pack to only the really essential ones, so I've removed these and moved them to a section of the readme where they're still recommended but just no longer installed by default.

x-ref nextflow training: nextflow-io/training#539 (comment)

[jfy133]

Although I use all 3 regularly I can see the logic:

1. Indent colouring - most of the languages we use don't care about indentation (except tools)
2. Spell check - we don't have a specific language requirement so sort of useless for standardisation

But I would argue to keep the TODO tree

3. Because we use a LOT of TODOs in many places in the template so it helps discover ability of these

[ewels]

Yup - also indent colouring annoys me with hanging indentation in nextflow, which looks super ugly.

Happy to keep TODO tree. I use that one quite a bit, just removed it to be consistent but can add it back again.

[ewels]

@jfy133 updated ✅