feat: taxonomy patch instead of re-generating

[alexgarel]

• adding a modified property
• adding lines location of entries
• keeping removed entries

The goal is to be able to patch taxonomy text files instead of re-generating them completely

Relates to: #541 and #366

TODO:

• [ ] be able to patch taxonomy to generate the PR
• [ ] add tests
• [ ] add modified parameter in search
• [ ] add sort on modified parameter in search