Start a new database, insert 1 document in it. Now shutdown the database and run mongod --repair --repairpath <>. This immediately crashes with
c:\mongo\mongodb-win32-x86_64-2.0.1\bin>mongod.exe --repair --repairpath c:\data\repair
Fri Nov 11 13:28:10 [initandlisten] MongoDB starting : pid=7752 port=27017 dbpath=/data/db 64-bit host=Sridhar-PC
Fri Nov 11 13:28:10 [initandlisten] db version v2.0.1, pdfile version 4.5
Fri Nov 11 13:28:10 [initandlisten] git version: 3a5cf0e2134a830d38d2d1aae7e88cac31bdd684
Fri Nov 11 13:28:10 [initandlisten] build info: windows (6, 1, 7601, 2, 'Service Pack 1') BOOST_LIB_VERSION=1_42
Fri Nov 11 13:28:10 [initandlisten] options:

Fri Nov 11 13:28:10 [initandlisten] journal dir=/data/db/journal
Fri Nov 11 13:28:10 [initandlisten] recover : no journal files present, no recovery needed
Fri Nov 11 13:28:11 [initandlisten] ****
Fri Nov 11 13:28:11 [initandlisten] ****
Fri Nov 11 13:28:11 [initandlisten] need to upgrade database test with pdfile version 4.5, new version: 4.5
Fri Nov 11 13:28:11 [initandlisten] starting upgrade
Fri Nov 11 13:28:11 [initandlisten] test repairDatabase test
Fri Nov 11 13:28:11 [initandlisten] removeJournalFiles
Fri Nov 11 13:28:11 [initandlisten] warning file is not under db path? c:/data/repair/$tmp_repairDatabase_3/test /data/d
b
Fri Nov 11 13:28:11 [initandlisten] warning file is not under db path? c:/data/repair/$tmp_repairDatabase_3/test.ns /dat
a/db
Fri Nov 11 13:28:11 [initandlisten] warning file is not under db path? c:/data/repair/$tmp_repairDatabase_3/test /data/d
b
Fri Nov 11 13:28:11 [initandlisten] warning file is not under db path? c:/data/repair/$tmp_repairDatabase_3/test.0 /data
/db
Fri Nov 11 13:28:11 [initandlisten] build index test.foo

Fri Nov 11 13:28:11 [initandlisten] build index done 1 records 0.005 secs
Fri Nov 11 13:28:11 [initandlisten] Assertion failure _recovering db\dur_recover.cpp 235
Fri Nov 11 13:28:11 [initandlisten] dbexception in groupCommit causing immediate shutdown: 0 assertion db\dur_recover.cp
p:235
Fri Nov 11 13:28:11 gc1

Note: If you run mongod --repair --repairpath --nojournal this does not occur