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fix: soft delete empty repository records (batch 1)

João Pereira requested to merge 570-step_2_of_4_mr_1 into master

Related to #570 (closed). This is part of step 3 of 4 as described in #570 (comment 818150257).

We're doing a batch update as first described in #570 (comment 838050935). This MR is for batch 1, which will be a very small batch (1000 records) to guarantee that everything works OK. We'll then increase the batch size and do multiple batches per migration/release.

Edited by João Pereira

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