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When you select a different root part, it does not account for all of the stages and miscalculates mass.
Below are 2 examples.
First is a fuel tank being the root part, in the 2nd of the 3 stages that provides thrust. Here it is ignoring the stage above the root part and its mass. I saved and reloaded this craft, and the error did not correct itself. I've checked the staging order and it is still correct like it is control craft above.
Second is a fuel tank being the root part on the last thrust providing stage, with only the command pod and its separator above it. Here it does not account for the command pod attributing to the mass of the stage. Like in the example above, I saved and reloaded this craft, and the error did not correct itself. I've checked the staging order and it is still correct like it is in the control craft.
Whenever you cut your vessel in half by decoupling, the simulation must make an assumption which part it should focus on afterwards. The rule used here is "always follow the root part". It also assumes that you will stage in a way to maximise the deltaV of this vessel.
So if the pod is root, everything works as expected.
Now suppose the root is a first-stage booster. The first staging lights it. The second staging decouples it from the rest of the vessel. So the 'optimal timing' for max deltaV would be to light it and immediately stage again to decouple it like a missile.
I would say this is intended behavior because it gives you freedom to tell the simulation what to calculate. And the simulation probably needs this kind of guidance because it is a very complex and error-prone task to interpret how a vessel is supposed to be used.
I think using "follow the root" isn't the best way to to calculate ship data, because people may set the root part to a first stage tank or near CoM for structural reasons. It should follow whatever part has the default command control, the command part that was placed first. This way people who start their craft with their primary command part and change the root later have accurate Engineer data by default.
This was all tested in a fresh install of 0.90 / 32bit with Kerbal Engineer being the only mod installed.
With the root part being the command pod, mass is calculated normally. This is the control craft for the test.
https://i.imgur.com/ZTIa1es.png
When you select a different root part, it does not account for all of the stages and miscalculates mass.
Below are 2 examples.
First is a fuel tank being the root part, in the 2nd of the 3 stages that provides thrust. Here it is ignoring the stage above the root part and its mass. I saved and reloaded this craft, and the error did not correct itself. I've checked the staging order and it is still correct like it is control craft above.
https://i.imgur.com/YvGdSmp.png
Second is a fuel tank being the root part on the last thrust providing stage, with only the command pod and its separator above it. Here it does not account for the command pod attributing to the mass of the stage. Like in the example above, I saved and reloaded this craft, and the error did not correct itself. I've checked the staging order and it is still correct like it is in the control craft.
https://i.imgur.com/JzDpHv6.png
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