It's a bit of a mess. I talked with Ili about this, and we've both agreed that the non-rare materials in there will be better put to use in gil form.
I've volunteered to sell off the stock and dump 100% of the proceeds back into the guild bank as gil, as I am currently paying for four retainers, but using the sales space of only two for my own purposes.
If you plan to use anything in there for your own crafting or whatever, be sure to pull it before it becomes gil! I will be leaving some things, including, but not limited to, materia, gardening items, crystals, myth items, and otherwise rare or hard to get things that we're likely to use in the future.
If you donated a lot of stuff, do not fret - your contribution will, now in the form of gil, go towards a big guild house (we're closer than you'd think - merely waiting for the next housing block to be released), chocobo stuff, gardening, etc.
Voclain Praux replied
560 weeks ago