These messages are caused by common misunderstanding of the Prolog interactive toplevel. Both :-/1 and ?-/1 are used to specify queries. If some text reads

?- prove(X).

then the ?- is the prompt and should not be typed. Repeating the prompt results in:

?- ?- prove(X).
ERROR: Undefined procedure: (?-)/1
ERROR:   ?- is the Prolog prompt
ERROR:   See FAQ at http://www.swi-prolog.org/FAQ/ToplevelMode.md

Terms that you enter at the toplevel are processes as queries, while terms that appear in a file that is loaded into Prolog is processed as a set of rules and facts. If a text reads as below, this is a rule.

carnivore(X) :- animal(X), eats_meat(X).

Trying to enter this at the toplevel results in the error below. Why? Because a rule is a term :-(Head, Body), and because the toplevel interprets terms as queries. There is no predicate with the name :- and two arguments.

?- carnivore(X) :- animal(X), eats_meat(X).
ERROR: Undefined procedure: (:-)/2
ERROR:   Rules must be loaded from a file
ERROR:   See FAQ at http://www.swi-prolog.org/FAQ/ToplevelMode.md

Isn't this stupid? Well, no. Suppose we have a term eats_meat(rataplan). If this appears in a file, it states the fact that rataplan eats meat. If it appears at the toplevel, it asks Prolog to try proving whether rataplan eats meat.

If a text reads

:- use_module(library(clpfd)).

This is a directive. Directives are similar to queries, but instead of asking the toplevel to do something, they ask the compiler to do something. Like rules and facts, such terms belong in files.

Can I add rules and facts from the toplevel?

Yes. There are two ways. One is to consult user, as illustrated below. Where is says <EOF>, you must type the character for end-of-file, which is Control-D on most systems.

?- [user].
|: carnivore(X) :- animal(X), eats_meat(X).
|: <EOF>
% user://1 compiled 0.00 sec, 880 bytes
true.

The second way is by using assert/1. Note that these two mechanisms do not mix for the same predicate. See DynamicCode.md.

?- assert((carnivore(X) :- animal(X), eats_meat(X))).

We advice to use an editor to make a file with rules and load this using the command below. Prolog files use the extension .pl, which you do not have to specify for loading the file. You may use any other extension, but this requires you to add the extension and quotes to turn this into valid Prolog syntax. For example: ?- ['myfile.md']..

?- [myfile].

Note that you can easily update your rules by editing the file and typing the command below. The make/0 predicate reloads all files that have been modified, replacing old rules loaded from that file with the current content of the file.

?- make.

Can I put queries in files?

Yes. As we have seen above, there are directives for the compiler that are written as :- Term. Here, Term must be recognized as a valid directive by the compiler (SWI-Prolog doesn't enforce this, but some other Prolog implementations do). You can specify arbitrary Prolog code that is executed after loading the file using initialization/1 e.g.,

:- initialization
   format('Hello world!~n').

SWI-Prolog also defines initialization/2, where the second argument defines when the goal is executed. Notably main defines the goal as the entry point of the program. See RunProgram.md.