make -X option accessible from treebest phyml

Fix stripping of [&&NHX]

`treebest best` was creating "empty" [&&NHX] features in nhx output files,
which break downstreaming tools, e.g. ETE3.

To replicate the problem:

```
treebest best -f test_tree.nhx -o output.nhx test_msa.fasta
```

using input files available on:

https://gist.github.com/nsoranzo/4d34e2e3dd7fc3a44157534fa647d64e

which would create the file output.nhx containing a line like this:

```
(ENSOCUT00000008795_Oryctolaguscuniculus:0.060686[&&NHX],
```

After applying this patch, the output line will instead be:

```
(ENSOCUT00000008795_Oryctolaguscuniculus:0.060686,
```

New parameter to return immediately after having created the filtered…

… alignment

algo.h now uses standard libs (no "extern" ref.)

bugfix: Bison can crash if YYINITDEPTH is too small.

This would cause TreeBeST to fail while parsing the newick file.

Exit code 0 should only be for success

Exit code 0 should only be for success

Exit code 0 should only be for success

Exit code 0 should only be for success

Exit code 0 should only be for success