There are a variety of additional scripts that are included with the
JRuby installation that use JRuby itself.

For instance the `bin/gem` had the following contents:

```bash
❯ cat /nix/store/kglkqf56ii83yl6yrgcaj5r3s9m2fzr0-jruby-9.2.13.0/bin/gem

load File.join(File.dirname(__FILE__), 'jgem')
```

This is clearly wrong. Patchshebangs was not picking up the fix as part
of stdenv because the patch is not a build input but the final output
itself.

We have to rely on substituteInPlace so that we get the correct version.

```bash
❯ cat /nix/store/k4fnrn0dcsh2wzw81217r0ywsspb468f-jruby-9.2.13.0/bin/gem

```

https://github.com/traviscross/mtr/blob/v0.94/NEWS

cddlib: 0.94j -> 0.94l

mtr: 0.93 -> 0.94

cliquer: 1.21 -> 1.22

Fix shebang for binaries in JRuby

dbeaver: 7.2.0 -> 7.2.1

cytoscape: 3.8.0 -> 3.8.1

amber: init at unstable-2020-09-23

go-toml: 1.8.0 -> 1.8.1