At first I made some simple changes for Flagship weapons and other stuff:
Changes in v2.5
New list of augments for Flagship:
- First stage: Zoltan Shield, Slug Repair Gel, Engi Medbots.
Second stage: Reverse Ion Field, Engi Medbots, Rock Plating.
Third stage: 2x Automated reloader, Rock Plating.
Changes in v2
Some augments (Titanium System Casing, Zoltan Shield, Reverse Ion Field + Shield Charge Booster on last stage) added.
Flagship now use defense drone mk2 instead of mk1 on second stage.
Flagship has 999 drone parts on second stage
Hull up to 22 in all stages
Changes in v1
Boss Ion:
Fires 3 shots, 1 ion damage. Projectiles deal ion damage to shields, penetrate them and deal extra ion damage to systems. Low fire chance added.
Boss Laser:
Replaces old Boss Beam. Fires 5 shots, 2 damage each.
Boss Missile:
Unchanged.

Boss Beam:
Replaces old Boss Laser. Beam deal 1 damage, penetrates all shields + high breach chance, but has long cooldown.
Note: Every version is a standalone mod. If you want use specific version you should download archive and install files which you need.