Update cli.rst

[sooyounga]

updated to include --yes flag in the docs based on https://github.com/ReproNim/neurodocker/issues/508

• did not change the help messages in the python files, but it can be if needed?

added other missing flags, including --json flag, as well as missing options and versions, etc. from checking diff with what the neurodocker generate docker --help command generates currently

[codecov[bot]]

Codecov Report

Patch coverage has no change and project coverage change: -0.02 :warning:

Comparison is base (e766064) 88.77% compared to head (d291420) 88.75%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #514 +/- ## ========================================== - Coverage 88.77% 88.75% -0.02% ========================================== Files 11 11 Lines 1033 1032 -1 ========================================== - Hits 917 916 -1 Misses 116 116 ``` | [Impacted Files](https://codecov.io/gh/ReproNim/neurodocker/pull/514?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=ReproNim) | Coverage Δ | | |---|---|---| | [neurodocker/cli/generate.py](https://codecov.io/gh/ReproNim/neurodocker/pull/514?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=ReproNim#diff-bmV1cm9kb2NrZXIvY2xpL2dlbmVyYXRlLnB5) | `91.62% <0.00%> (-0.04%)` | :arrow_down: | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=ReproNim). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=ReproNim)

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[djarecka]

@sooyounga - looks good, but could you also check if the neurodocker generate singularity --help has changed?