[doc] Improve documentation for binaries

[woshilapin]

Ref. ND-929

[pbougue]

The point of this PR as I understood it was to have all sub-readme very similars.

Any diff with gtfs2netexfr/README.md should be just about specificities of the bin:

• If using proj, the topo should be the same (no mention of the version, just in main readme)
• adding/removing specific required params
• same topo on the NeTEx manual-check (link will change with [doc] Improve contributing #665 : rebase!)
• Maybe some other diffs I didn't spot for restrict or ntfs2ntfs ?

So current work is good for me, but I think there is a little more changes to do on sub-readmes.

[woshilapin]

The point of this PR as I understood it was to have all sub-readme very similars.

Any diff with gtfs2netexfr/README.md should be just about specificities of the bin:

* If using proj, the topo should be the same (no mention of the version, just in main readme)

* adding/removing specific required params

* same topo on the NeTEx manual-check (link will change with #665 : rebase!)

* Maybe some other diffs I didn't spot for `restrict` or `ntfs2ntfs` ?

So current work is good for me, but I think there is a little more changes to do on sub-readmes.

So, here is the last modifications I made:

• I remove the section about configuration in gtfs2ntfs/README.md (it is already covered by the --help option
• I removed the PROJ version from ntfs2netexfr (already mentioned in CONTRIBUTING.md)
• I added a link to the section check the output manually in ntfs2netexfr (and I rebased for that)