Can you provide more details, so we could reproduce the problem? It works for me with sqlite:
$ cat test.sql
create table boo (id integer primary key, name text);
create table foo (id integer primary key, boo_id integer, foreign key
+(boo_id) references boo(id));
$ sqlite3 test.db <test.sql
$ dbicdump Foo dbi:SQLite:test.db
Dumping manual schema for Foo to directory . ...
Schema dump completed.
$ grep -RE "belongs_to|has_many" .
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