Would you consider adding a --anchor-vc-ignore option to gnulib-tool? This option would tell gnulib-tool to precede every .gitignore entry it creates with "/" so that, as with .cvsignore, the entry would not apply recursively to subdirectories. In Bison, we're anchoring all .gitignore entries in this way.
For .gitignore files generated by gnulib-tool, I think that should be the default.
Paolo
