One further piece of the mystery I see now:

The "View Data tables Registry" shows my tool's loc files, but has odd stuff 
for "Tool data path" and "Missing index file" columns, for example:

   blast_reporting_fields [tab] 
 [tab] /usr/local/galaxy/test/galaxy-dist/tool-data
   ./database/tmp/tmp-toolshed-gmfcrDITxyK/blast_reporting_fields.loc [tab] 
./database/tmp/tmp-toolshed-gmfcrDITxyK [tab] missing

There is no galaxy-dist/database/tmp-toolshed-gmfcrDITxyK folder, if that's 
where its supposed to be? Is there some setting for database tmp folder cache 
for tools?

Thanks for tips ...

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