R&D

Chigara can upgrade various aspects of friendly units if sufficient funds are allocated to research. The cost of subsequent upgrades rise quickly (furthermore the rise depends on the unit, for example the Phoenix armor upgrades after the first are a lot more costly that the same ones for the Sunrider), but the player has a lot of flexibility as to what aspects of what units he wants to improve. Perhaps one would rather cover weakness and focus on defense and HP, or perhaps another one discovers powerful combinations of upgrades that synergize very well in battle.

Hull Plating
Increases maximum HP of a ship by 100.

Energy Reactor
Increases maximum EN of a ship by 5, which allows for either more attacks and more movement.

Evasion
Decreases the chance this unit gets hit by enemy attacks (increases evasion by 5)

Weapons
Kinetic, Energy, Melee and Missile weapons are upgrades separately from each other, but the effects are similar.

Damage
Each upgrades raises the base damage of affected weapons by 5% (10% for missiles). This increase is multiplicative with any buffs on the same ship, enhancing the effect of both.

Accuracy
Each upgrade increases the base accuracy of affected weapons by 5%. This is not an added bonus to chance-to-hit like an accuracy buff is, and is therefore more effective the higher the base accuracy of a weapon is.

Missiles already have very high accuracy, so instead they have an upgrade that decreases the enemy's effective flak rating.

Energy cost
Each upgrade reduces the EN cost of affected weapons by 5% (10% for missiles). Combined with extra EN upgrades this can give a unit the ability to fire her weapons multiple times during a single phase.

Shield Power
If the unit is capable of producing an energy field this upgrade can increase the strength of the generated field by 5 points. Every unit affected by the field gains the extra effect provided by the upgrade

Shield Range
A very expensive and very powerful upgrade that increases the range of the unit's shields by 1.

Flak
Increases the chance of intercepting an enemy missile or rocket by an additional 5% per upgrade

Armor
Decreases the damage received per hit by 5 per upgrade (increases armour by 5)(Note that only the Sunriders armour increases by 5, your other units armour only increases by 1). This extra armor gets reduced in effectiveness relative to the unit's HP level just like the default armor is.

Repair Crew
it's a secret to everybody.