add note to orthoxml to keep track of filtering

[sinamajidian]

After filtering an orthoxml file by completeness score, we could update the header to inform the user about the history of the file. For BAM and VCF files, they usually keep adding all the command lines in the pipeline to the file that is being edited.
It's not good to modife the orign or originVersion attributes

<orthoXML xmlns="http://orthoXML.org/2011/" origin="FastOMA 0.3.4" originVersion="2024-10-15 22:12:08" version="0.5">

but Adrian is suggesting that we could use the element that is allowed after the root element. This would at least be valid and would not break any of the downstream tools.

<orthoXML xmlns="http://orthoxml.org/2011/" origin="FastOMA" version="0.5">
   <notes>
     <filter tool="OrthoXML-tools" command="orthoxml-tool  filter --completeness=0.3"/>
   </notes>
   <species>...
</orthoXML>

This could be a good feature to add as a note to orthoxml, so a user can keep track of how the orthoxml file is changed or filtered. We faced the issue that after being away from the project for some months, we didn't remember whether the orthoxml file was the raw output of FastOMA or it was filtered.