Dear Evan,

But, since the time delay can be significant (depending on how many
fonts you're working with), this is somewhat more than a nuisance.
Further, there is clearly a 'bug' - perhaps not fatal, but one that
suggests that something needs a fix.

I will upload a new version fixing this (more precisely reverting the previous change) today on CTAN.

Commenting out

fonts.define.resolvers.file = fonts.define.resolvers.name

from luaotfload.lua seems to work, but

1\ what exactly does commenting this line out prevent? (Just for my
edification)

It will break fonts that are present in the font name database (which includes fonts reachable by fontconfig) but are not reachable by kpse, if you call them with the file: lookup. This means less fonts found. But if it worked before, it will certainly continue to work with the new version (without rebuilding the database too often).

2\ is this something that is going to be fixed in a more permanent way?

While I'm not entirely uncomfortable with the 'so long as it works'
approach to fixes, I'm even more comfortable with a real fix. I'm
holding off updating all my other systems until such time.

A real fix is present in the development branch, but it cannot reach CTAN before an update of several packets (fontspec, unicode-math and microtype mainly). Patches have been sent to the maintainers, some responded, others not... we hope it will reach TeXLive 2013, but it's not entirely depending on us!

Thank you,
--
Elie

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