Frequently (enough to become a problem) the agent will make changes not requested, guess at stuff and generally "over do it" necessitating a "rollback request" i.e. instruct the agent to revert its last changes.
More often than not it will attempt to checkout/pull the file in question from github
"without checking if there are unstaged changes"
If not paying close attention (or allowed github commands to run without confirmation) this can blow away significant amounts of work.
It will also try to pull the latest version if it mangles a file (I actually suspect vscode is doing the mangling)and it (the agent) is too lazy to fix it properly.
Basically:
"update boost instructions to specify git status must be checked before pulling files"