Some comments:
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It is important to distinguish between a function and the value of a function. Given f is a function then f(x) is a value of that function, and so too is f(t) or f(42) etc. When we define a function we define the action resulting in its value and the variable we use is arbitrary. Thus for example saying f(x) = 2x+3 defines the function f in exactly the same way as saying f(z) = 2z+3 or f(t) = 2t+3. The use of different variable names is immaterial. The use of y=f(x) is a means of defining the graph of the function as a set of points (x,y) satisfying y=f(x) or equivalently the set of points (t,f(t)) (z,f(z))...
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In the notation for definite integrals (which are values, not functions) the variable of integration is meaningful only inside the the integrand. It is exactly the same as summation notation where the index should only appear inside the summand.
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So take a function f and define another function A from it by defining the value of that function using a definite integral involving f:
[itex]A[/itex] is the function mapping the number [itex]x[/itex] to the value [itex]A(x)[/itex] given by the definite integral:
[tex]A(x) = \int_a^x f(t)dt[/tex]
Then the fundamental theorem states that the derivative of A is the function f, i.e. A' = f.
Note that it is NOT correct to say that "the derivative of A(x) is the function f(x)" which is trying to take the derivative of something which is NOT a function and identifying it with another something which is NOT a function.
Now we can speak of the derivatives of variable expressions but only when we are thinking of those expressions as functions of a specific independent variable. Thus we can speak of the derivative of f(x) with respect to x, and similarly we can speak of the derivative of f(g(x)) or x f(x) w.r.t. x.
We are using a function (or functions) to write and expression in x which is itself a function of x.
[edit] Thus it is OK to say: "The derivative of A(x) with respect to x, is f(x)". [end edit]
It's a subtle distinction but if ignored it leads to the confusion expressed in the O.P.