To Write Against . . .

To write against something could mean to dispute something:
Disputation of Dr. Martin Luther Concerning Penitence and Indulgences.

Or take the Cluetrain Mainfesto: its writings are against outdated, patronizing marketing methods which are, nevertheless cheerfully being sold to and paid by those who rather fail than cease to patronize us, THE PEOPLE.

But what does "writing against a directory mean?" This is shorthand for:

When a developer works with a shared directory - one that several editors use concurrently - and then commits the most recent version of a given file to that said directory, she could be said to write against that direcory.

Joanna committed her file commit_this.xsl to the directory Directory, already containing the file commit_this.xsl. This way she wrote against the directory.

Jan created a new file, brand_new.xsl in the directory Directory, he also wrote against the directory.