I've recently tried a couple of things, unsuccessfully, to fix the problem on 
my own. Make no mistake, this is flailing. I have little understanding of what 
I am doing, but in the absence of expert support....
1) I downloaded an older copy of the Thunderbird-Beagle add-on, version 0.1.2 . 
Same problem. Reinstall thunderbird-beagle 0.1.3.
2) I edited the contents of 
/usr/lib/thunderbird/extensions/{b656ef18-fd76-45e6-95cc-8043f26361e7}/chrome/beagle.jar
 in the following way:
a) sudo file-roller
b) open the file
c) gedit beagleIndexer.js
d) Based on a discussion I read ( 
https://bugzilla.gnome.org/show_bug.cgi?id=530632 ), describing a possible fix 
to the extension for Thunderbird 3 [Note: I am still using TB 2], I replaced 3 
instances of "path.unixStyleFilePath" with "nativePath" . Save. Okay to update 
the jar. Close.
e) This produced Exceptions in the Beagle Log that I did not used to have. 
Basically, it broke the Beagle backend. Reinstall thunderbird-beagle to undo 
the changes to beagleIndexer.js .
f) What we learn from this experience is that Beagle's Index Helper process 
apparently runs Mono to re-open Thunderbird's folders and read the contents. If 
this is so, the locus of the main problem (i.e., not indexing e-mail content) 
is the Beagle backend rather than the Thunderbird add-on. That is a body of 
code that I dare not touch. It's too bad, though, that the add-on does not just 
dump the e-mail content while it has the chance.

** Bug watch added: GNOME Bug Tracker #530632
   https://bugzilla.gnome.org/show_bug.cgi?id=530632

-- 
Beagle does not index Thunderbird mails
https://bugs.launchpad.net/bugs/221073
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