Changes in docs for Issues #4800, #3709, #3573, #2211 and PR #2414 (#5656)

* Changes in docs for Issues #4800, #3709, #3573, #2211, #521 and PR #2414

- Added section about `extras` in `dependency-specification.md` (#2414)
- Added note about VCS inclusion and exclusion in `include`/`exclude`
sections of `pyproject.toml` (#4800)
- Added link to dependency specification in `add` command documentation
(#3573)
- Added more info on default behaviour and cleaned up
`virtualenv.in-project` setting documentation (#3709)
- Added missing configuration options to `configuration.md` (#2211)

Co-authored-by: Arun Babu Neelicattu <arun.neelicattu@gmail.com>