I realize that the question was asking about EASA, but perhaps an FAA perspective will increase understanding. The FAA Pilot Controller glossary defines clearance as:
AIR TRAFFIC CONTROL CLEARANCE [ICAO]− Authorization for an aircraft to proceed under conditions specified by an air traffic control unit.
Note 1: For convenience, the term air traffic control clearance is frequently abbreviated to clearance when used in appropriate contexts.
Note 2: The abbreviated term clearance may be prefixed by the words taxi, takeoff, departure, en route, approach or landing to indicate the particular portion of flight to which the air traffic control clearance relates.
In short, clearance is permission, and is generally associated with operating under IFR in controlled airspace.
I will disregard taxiing at a tower controlled field because it can be done under IFR or VFR. Additionally, I have heard compelling arguments that you are not “cleared” to taxi, but are given taxi “instructions”. (Ground controllers will never use the word “cleared” when telling you to taxi).
But that is a separate discussion...
The process begins with filing an IFR flight plan. This notifies ATC of your intentions, and gives them time to enter your request into the system.
The actual clearance is issued when you call them, (radio at towered field, land line at uncontrolled field) field and put your clearance “on request”. When you call, ATC will issue the clearance. It will be either what you filed for, or it may contain amendments.
In the clearance you may be told to expect radar vectors. This then becomes part of your clearance. However, vectors assigned as needed during flight for traffic separation aren’t generally considered an amendment to the clearance. Think of them more as a temporary detour around something.
For example, if ATC needs to amend your clearance they will tell you specifically that they have an amendment, and ask when you are ready to copy. The amendment will generally be a rerouting that you are expected to follow on your own, and may also include a different altitude.
If given a vector, however, the expectation is that is it a temporary heading needed by ATC to provide traffic separation. Once the need for positive ATC control is past they will clear you to resume your own navigation along your flight planned route.