Ronan: I think that the primary cause of your misunderstaning is not knowing what exactly is considered "invalid input". But before I explain that further, please read this explanation that I wrote for Preben regarding callseq_only:

@Preben Alsholm I think that you don't fully understand the purpose of callseq_only. (If you did already understand what I say below, then I apologize, and please let me know.) It's only purpose is to discriminate between different sources of errors beginning with "invalid input"; it has no influence on other errors. This is shown in the examples of help page ?overload.

The overload mechanism reacts only to errors that begin with "invalid input". The following 2 things are always true, regardless of any options:

1. A procedure that is passed an argument that isn't allowed by its calling sequence will return an error beginning with "invalid input".
2. A procedure may also return an error beginning with "invalid input" for some other reason. There are three possible ways (that I can think of right now): 
   a. The error came from another procedure called within the procedure.
   b. The programmer has explicitly put "invalid input ...." in an error command which was executed.
   c. (This is the case that is most relevant to this Question:) The error is caused by the procedure attempting to use a parameter for which no argument has been passed.

If a procedure has option overload, then we need to decide whether both 1 & 2 cause passage to the next procedure in the overload, or whether only 1 causes it. If you only want 1, then use option overload(callseq_only). Then type 2 errors (including type 2c) will be treated as normal errors, not triggers for the overload mechanism.

I don't think that there's any bug here, but I may change that opinion if you post your "contrived example".

Ronan: From reading the thread after Preben's Answer, I think that you now understand that failure to pass an argument to match a parameter is not necessarily an error (of any kind). And I think that you also now understand that it only becomes an error if the procedure's execution path tries to use the parameter whose argument is missing. Now, to complete your understanding, you need to know two more things:

1. When such an error occurs, it is an "invalid input" error.
2. Whether it triggers the overload mechanism depends on whether you used callseq_only.

Let me know if this does what you want:

`value/&||`:= (a,b)-> normal(a*b/(a+b))
:
`print/&||`:= proc(A,B)
uses T= Typesetting;
    T:-mrow(T:-Typeset(A), T:-mo(" ∥ "), T:-Typeset(B))
end proc
:
R1 &|| R2 &|| R3;
     R1 || R2 || R3
value(%);

The ∥ is the HTML code for the double vertical bar.

There is no list indexing needed at all:

restart;
X:= eval(
    <
        1,             -X3_3/2 - 1/2, 0,   -X2_3;
        -X3_3/2 - 1/2, -2*X3_4 - 1,   X2_3, 0   ;
        0,              X2_3,         X3_3, X3_4;
        -X2_3,          0,            X3_4,    1
    >,
    [X3_4, X3_3, X2_3]=~ [1-A^2, -1-A^2, A*(3*A^2 - 1)] /~ (3*A^2 - 1)
);     
andseq(
    andseq(
        is(e::nonnegative),
        e= LinearAlgebra:-Eigenvalues(eval(X, A= r))
    ), 
    r= solve(A^3 - A)
);

I wasn't sure about your question #3. The above returns true iff all 12 eigenvalues are real and nonnegative. Any variation of that that you want can also be done without indexing.

Note that is(e::nonnegative) is sufficient to check whether e is real and nonnegative.

Change dis play to display.

Here is a simple solution using select:

M3[select(M3[.., 3]=~ 2, [$op([1,1], M3)])];

To select columns whose 2nd row is 80 (for example), do

M3[.., select(M3[2]=~ 80, [$op([1,2], M3)])];

In either case, the = can be replaced by any of <, <=, >, >=, in, or <>.

For 2D Input, you need to put 1.. after $, as in 

M3[.., select(M3[2]=~ 80, [$1..op([1,2], M3)])];

Appending assuming complex is sufficient to remove the guaranteed nonzero factors in this case. A simple procedure for it is

Simp:= (q::`=`)-> local e:= factor((lhs-rhs)(q));
    `if`(e::`*`, (remove(f-> is(f<>0), e) assuming complex), e) = 0
:
eq:= diff(v(x),x,x)*exp(x^2) = 0:
Simp(eq);

You could change complex to real if you want.

Like this:

T:= Typesetting:
plots:-textplot(
    [1, 2, T:-mover(T:-msub(T:-mi("u"), T:-mn("1")), T:-mo("&rarr;"), 'mathcolor'= 'red')],
    'align'= {'above', 'right'}, 'font'= ["ARIAL", 'BOLD', 16]
);

You need to change s(e+i) to s*(e+i).

And although it doesn't cause a problem here, please don't use with(linalg).

It can be done like this:

restart:
model:= [x^2*y*alpha[1, 11], x*z^2*alpha[2, 15], y^2*z*alpha[3, 17] + y*z*alpha[3, 8]]:
M:= [
    alpha[i, 0], alpha[i, 1]*x, alpha[i, 2]*y, alpha[i, 3]*z, alpha[i, 4]*x^2, 
    alpha[i, 5]*y*x, alpha[i, 6]*z*x, alpha[i, 7]*y^2, alpha[i, 8]*z*y, alpha[i, 9]*z^2,
    alpha[i, 10]*x^3, alpha[i, 11]*y*x^2, alpha[i, 12]*z*x^2, alpha[i, 13]*y^2*x, 
    alpha[i, 14]*z*y*x, alpha[i, 15]*z^2*x, alpha[i, 16]*y^3, alpha[i, 17]*z*y^2, 
    alpha[i, 18]*z^2*y, alpha[i, 19]*z^3
]:
#Construct new models as a list of lists:
models:= CodeTools:-Usage([
    for i,m in model do
        map(subs, m=~ m+~ subs({`if`}(m::`+`, op(m), m)=~ (), M), model)[]
    od
]);
memory used=41.66KiB, alloc change=0 bytes,
cpu time=0ns, real time=0ns, gc time=0ns
#Lenghty output omitted
nops(%);
                               56

The lines

p2 := with(plots);
inequal(58 < x, x = 0 .. 100, y = 0 .. 2);

should be changed to

with(plots):
p2:= nequal(58 < x, x = 0 .. 100, y = 0 .. 2);

I suppose that vmcofs is very large (millions of numeric entries or tens of thousands of symbolic entries), and you don't need to save every slice? Is that right? 

Create a module that contains a single export, a table:

VM:= module() export vmcofs::table:= table(); end module;

Then every time that you have a slice k that you want to save, instead of doing savelib, do instead

VM:-vmcofs[k]:= vmcofs[k];

When you're done choosing slices, save the whole module with

savelib(VM, lib);

If you change any entries in the array vmcofs[k] after putting that slice into the table but before using savelib, then the table will automatically contain the newly updated slice k, not the original slice k, and only the updated one will be saved to the library. If you don't want this to happen, let me know.

The module is superfluous in this simplistic version; all that's needed is the table. I just included the module because you might find it useful later (for storing other info related to your project). The added overhead for using a module is infinitesimal.

A module with no locals, only exports, is also called a Record. You can create it with the Record command, if you wish. It hardly makes any difference.

Since test is not a reserved word and doesn't contain any special characters, the backquotes don't do anything: test and `test` mean exactly the same thing. So yes, you're right, the help page's usage of backquotes is unnecessarily confusing.

If I do it without Physics Updates, then there's no problem.

The type given as 2nd argument to subsindets can use a specific symbol by referring to it as identical(xi). So, this works:

S:= ex-> subsindets(ex, identical(xi)^integer, e-> H(op(2,e))*e);

Yes, the command is called maplemint.