$ mkdir test
$ cd test
$ fossil init test
project-id: 5545d1358dffb32424958343acc90220c6a03ec7
server-id:  6ba5d397e66d52d97fd97befc18ccbff8e19b37a
admin-user: joerg (initial password is "484064")
$ fossil sqlite3 test
fossil: use --repository or -R to specify the repository database
$ fossil sqlite3 -R test test2
SQLite version 3.7.4
Enter ".help" for instructions
Enter SQL statements terminated with a ";"
sqlite> vacuum;
sqlite> .quit
$ ls
test  test2

The -R should not be required and either not be accepted or complain if given both a repository as positional argument and via -R.

It would be nice if it accepted SQL commands as command line parameter like the standalone sqlite3 command. Handling EOF as implicit ; would be another minor improvement.