`flatten(sys)` and `namespace_equations` do not handle `connect` correctly

[baggepinnen]

Flattening a system that contains connect statements produces an invalid system

julia> structural_simplify(sys_outer)
Model outer with 7 equations
...

julia> structural_simplify(ModelingToolkit.flatten(sys_outer))
ERROR: ExtraVariablesSystemException: The system is unbalanced. There are 19 highest order derivative variables and 13 equations.
More variables than equations, here are the potential extra variable(s):
 F₊x(t)
 inner₊P₊x(t)
 inner₊P₊input₊u(t)
 inner₊C₊input₊u(t)
 inner₊add₊input2₊u(t)
 add₊input2₊u(t)
 C₊input₊u(t)
 P₊input₊u(t)
Stacktrace:

Connections like connect(P.output, add.input2) should have been turned into connect(inner.P.output, inner.add.input2)

julia> equations(ModelingToolkit.flatten(sys_outer))
18-element Vector{Equation}:
 connect(r.output, F.input)
 connect(F.output, inner.add.input1)
 F₊u(t) ~ F₊input₊u(t)
 F₊y(t) ~ F₊output₊u(t)
 Differential(t)(F₊x(t)) ~ (F₊k*F₊u(t) - F₊x(t)) / F₊T
 F₊y(t) ~ F₊x(t)
 connect(P.output, add.input2)
 connect(add.output, C.input)
 connect(C.output, P.input)
 inner₊P₊u(t) ~ inner₊P₊input₊u(t)
 inner₊P₊y(t) ~ inner₊P₊output₊u(t)
 Differential(t)(inner₊P₊x(t)) ~ (inner₊P₊k*inner₊P₊u(t) - inner₊P₊x(t)) / inner₊P₊T
 inner₊P₊y(t) ~ inner₊P₊x(t)
 inner₊C₊u(t) ~ inner₊C₊input₊u(t)
 inner₊C₊y(t) ~ inner₊C₊output₊u(t)
 inner₊C₊y(t) ~ inner₊C₊k*inner₊C₊u(t)
 inner₊add₊output₊u(t) ~ inner₊add₊k1*inner₊add₊input1₊u(t) + inner₊add₊k2*inner₊add₊input2₊u(t)
 r₊output₊u(t) ~ r₊k

This also applies to namespace_equations(sys)

[YingboMa]

Flatten shouldn't be used with connect. expand_connection does flattening as well has handling the namespacing.