fix(storage/git): Make git sync untracked work with sqlite.

[tsukasa-au]

The previous implementation of the sync untracked feature would attempt to run multiple queries in parallel. The knex framework appears to use a separate connection for each query by default (unless the queries are tied together by a transaction). When using sqlite, there is only a single connection available in the knex database pool, causing this feature to deadlock (when the initial query can not return all results immediatly).

In this change, we switch to doing all of these queries in a transaction, which causes all quries to occur on a single connection.