Q:

What is "=" in transcriptions of Hittite

I have not yet seen this double-hyphen explained, which is written eg. in An Etymological Dictionary Of The Hittite Inherited Lexicon (Kloekhorsts 2007)

-a (3rd.sg.pres.midd.-ending): see -a(ri)
=a 'and, too': see *=(i̯)a
=a 'but': see =(m)a
=a- (enclitic pronoun) 'he, she, it': […; pg. 196-198]

What's the difference from = to the usual hyphenation marking morpheme boundaries?

[…] The forms [n]=e-e=n (KBo 17.1 KBo 25.3 i 20 (OS)) and [n=e-e=]n (StBoT 25.4 i 15 (OS)) seem to show that […; pg. 208-209]

Wow, that's most cryptic. The question should be however easy to answer without detours into grammar (otherwise, pending own research, I would revise the question). Is the difference just ending versus enclitic?
How specialized is this, certainly not exclusive to Hittite studies?!

A:

Your guess is correct; the equals sign/double hyphen separates clitics from the words they attach to.
For example, from the Ten-Year Annals (KBo 3.4 ii 65):

nu=us=si=kan widār arha dahhun
  Then I took away the waters there.

nu  =us     =si     =kan widār        arha da  -hhun  
then=3PL.ACC=3SG.LOC=MOD water.ACC.PL away take-1.SG.PAST

This isn't exclusive to Hittite; it's actually part of the Leipzig glossing conventions (rule 2). It's just very prevalent in Hittite because Hittite uses a lot of enclitics—most sentences will have at least one, and four or five isn't unusual.
(Some sources, including the Chicago Hittite Dictionary, use a double oblique hyphen (⸗) instead; this has the drawback of being annoyingly difficult to type, so Leipzig recommends a plain ASCII equals sign.)

