Only select and de-select visible checkboxes

This avoids selecting checkboxes that are not visible due to filtering
by journalist designation. There was a hack to avoid accidentally
deleting collections that were selected, this fix replaces that with a
much cleaner and simpler solution which also prevents confusion by
seeing previously hidden items checked when clearing the filter text.
Merge pull request #641 from freedomofpress/fix-select-and-filter-interaction

Only select and de-select visible checkboxes