app-layer: improve/fix updates logic

app-layer: improve/fix updates logic

In 23323a961fac ("app-layer: reduce app cleanup and output-tx calls"), flag
was set per packet updating the app-layer state. However this was missing a
common pattern: in IDS mode most updates are done in the opposite direction
of the traffic due to updates getting triggered by ACK's. This meant that
file store processing might not happen for a long time, or at all. Also,
app layer cleanup might not be called, which includes file pruning.

This patch sets per flow set of flags to indicate app layer is (potentially)
updated. It sets this per direction, based on how the parsers were invoked.
If an ACK triggers an app update, the flow is tagged for the opposite
direction and the next packet in that direction triggers output and cleanup.

Fixes: 23323a961fac ("app-layer: reduce app cleanup and output-tx calls")
Bug: #6120.