Hello.
I agree with Chamade about the hybrid mode, to put it simply.
If the mode is active, you cannot reorder the surface and construction elements before the parent. (e.g. I create a plane // by a point I cannot reorder the plane in the tree before the point.)
These same elements can be included in part bodies with the same rule.
If the mode is idle, these elements cannot be included directly in a body and do not meet the parent organization rules.
It is important to know that it is extremely difficult to transform a hybrid model into a non-hybrid.
Skeleton.
For an assembly skeleton, I know two types.
ASS by compulsion.
The skeleton represents the position of the components in the assembly.
Each component is designed to be stored on the origin (e.g. for a screw, the axis of the screw on Z, the point of origin (X-0. Y-0; Z-0) is coincident with the bearing surface of the screw.
This type of assembly is very useful when there are a large number of parts that are standard components or machined library parts that can be used in other projects.
ASS In position.
The skeleton controls the position of the geometry of the components.
The origin of the assembly is common to most parts or sub-assemblies.
(this is where it is convenient to create markers) the published elements (marker or other) are copied and pasted with a link in their respective parts or subsets.
The only assembly constraint used for each part and sub-assembly is "fixity".
In each piece we design not on the common marker but on the one pasted with an "external ref" link.
From assembly, changing a position moves the geometry inside the part or S/E.
This type of assembly is widely used for injection molds (for example).
Remarks after opening your file.
There is an Inactivated formula (we very frequently have elements in a skeleton that we activate or inactive) so we have to be very careful, not to leave this type of elements if they are not necessary.
A few unnamed points.
You have to keep in mind that this will very quickly become a gas plant so use all the features of CATIA to simplify the skeleton (e.g. using the "surface workshop" symmetries it saves formulas etc if several lines, curve are intended for the same part the "assembly" surface function is very useful.)