I've noticed a number of doubled words (e.g. the the) in the doc files.

Here are my findings in the form file followed by a series of doubled word separated by comma.

sqlite-doc-3390200\appfunc.html,in in
sqlite-doc-3390200\consortium_agreement-20071201.html,at at
sqlite-doc-3390200\compile.html,the the
sqlite-doc-3390200\changes.html,is is,into into,one one,of of
sqlite-doc-3390200\capi3ref.html,the the,also also,the the
sqlite-doc-3390200\fileformat.html,stores stores,they they,number number
sqlite-doc-3390200\fileio.html,of of
sqlite-doc-3390200\fileformat2.html,stores stores,they they,number number
sqlite-doc-3390200\fts5.html,if if,into into
sqlite-doc-3390200\lang_altertable.html,some some
sqlite-doc-3390200\lang_expr.html,database database
sqlite-doc-3390200\lockingv3.html,file file
sqlite-doc-3390200\oldnews.html,cause cause		[maybe causes]
sqlite-doc-3390200\opcode.html,how how, the the
sqlite-doc-3390200\selfcontained.html,can can
sqlite-doc-3390200\search,the the
sqlite-doc-3390200\lang_select.html,syntax syntax
sqlite-doc-3390200\vtab.html,for for
sqlite-doc-3390200\c3ref\autovacuum_pages.html,the the
sqlite-doc-3390200\c3ref\backup_finish.html,also also
sqlite-doc-3390200\c3ref\c_checkpoint_full.html,for for
sqlite-doc-3390200\c3ref\hard_heap_limit64.html,the the
sqlite-doc-3390200\requirements.html,stores stores,they they,the the,number number
sqlite-doc-3390200\releaselog\3_36_0.html,is is
sqlite-doc-3390200\releaselog\3_3_14.html,one one
sqlite-doc-3390200\releaselog\3_8_2.html,into into
sqlite-doc-3390200\search.d\admin,the the
sqlite-doc-3390200\search.d\search.db		[multiples occurences]

I didn't put in line numbers, the relevant parts are trivial to find.