the manual way of making a manifest is
first copy the entrenchment's manifests into the mod's root folder,
then add each of the files you want to(note NEED EXACTLY the SamE Case in the entity as the file name otherwise minidump), while INCREASING the number at the top of the file,
and delete the entity files you do not want and decrease the count at the top of the file (but make sure the files removed are NOT referenced by any files that are left otherwise it will minidump).
the only reason that the manifest maker might not see your entrenchment is if it is stored in a different path to your sins as the mod assumes that sins, entrenchment AND diplomacy are all in the program files sins of a solar empire folder as the default install does place them, and it does look at the registry entry to find where sins is installed.
harpo