The current model for projects is that they increase the multiplier of the output type corresponding to the project, rather than creating raw output of the type corresponding to the project. Thus, in order to gain a benefit from running a project, you must have a nonzero slider setting towards the output type corresponding to the project. The bonus to the appropriate output multiplier granted by the project may be calculated as follows
B = 0.1 * ceiling([manufacturing output] / 10)
where B is the amount added to the appropriate output multiplier. Thus, if X is the basic output multiplier you get from planetary specials and improvements, starbases, civilization abilities, and anything else, the output generated when using a project may be calculated as follows:
[Output] = x * [production] * (1 + B + X)
where [Output] is your planet's output of the type corresponding to the project, [production] is your planet's base production, and x is the fraction of your planet's production dedicated to the appropriate output type. This means that if you have a planet where you could either dedicate x * 100% of your planet's production to an output type corresponding to a project and get a project bonus, or y * 100% of your planet's production bonus to that output type and not get a bonus from a project, the project is only worthwhile if the bonus B granted by it satisfies the condition
B > (1 + X) * ((y / x) - 1)
where B is the bonus granted by the project, X is the bonus granted to the output type corresponding to the project from all sources except the project and direct modifiers to base production (e.g. approval), y is the fraction of planetary production you would have dedicated to this output type had you not decided to use the project, and x is the fraction of the planet's production you would dedicate to this output type if you decide to use the project. An alternative formulation is
X < (x * (B + 1) - y) / (1 - x)
which gives you the maximum value of X, the bonus towards a project's output type, for which you will see an improvement in the total output of that type when using a project which grants a bonus of B, with x and y as defined above.
The minimum bonus you can get from a project is 10% as long as you have some positive manufacturing output; if you set 1% manufacturing and 99% to the desired output type, the maximum value of X for which you will see a net increase in output is X = +890%.
If you would like to restore the old project functionality, you can edit the entries in PlanetaryProjectDefs.XML in \Galactic Civilizations 3\Data\Game\; I would suggest replacing
<ManufacturingPerBonus>10</ManufacturingPerBonus>
<Bonus>
<EffectType>ColonyGrossIncome</EffectType>
<Target>
<TargetType>Colony</TargetType>
</Target>
<BonusType>Multiplier</BonusType>
<Value>0.10</Value>
</Bonus>
with
<ManufacturingPerBonus>0.1</ManufacturingPerBonus>
<Bonus>
<EffectType>ColonyGrossIncome</EffectType>
<Target>
<TargetType>Colony</TargetType>
</Target>
<BonusType>Flat</BonusType>
<Value>0.025</Value>
</Bonus>
for the economic project and a similar modification to the research project to restore the old functionality. The purpose of using 0.1 manufacturing per bonus is to minimize the effects of the ceiling function; you can use a smaller number and further reduce the effect, or you can use a larger number and live with the effects of the ceiling function, but if you do, remember to adjust the flat bonus of 0.025 to something appropriate for the amount of manufacturing you're using.
