ATC "clearance" is only used in specific situations:
- A route clearance - pilots request this when ready
- Takeoff clearance - pilots assumed to be ready unless they say otherwise
- Approach clearance - ATC provides this once the aircraft is positioned
- Landing clearance - ATC provides this when ready
All of these are very important details of the flight, and avoiding using the word "clearance" in other situations prevents confusion about what ATC has cleared the pilots to do. (There are others but for the typical commercial flight these are the main ones)
Anything else would be an instruction from ATC. Pilots may make requests but are expected to follow these instructions unless they feel that it would compromise safety.
Before the flight, the pilot will request their route clearance. ATC will respond by clearing them to fly to their destination via a certain route. This is usually the only clearance pilots receive before takeoff.
The pushback will be requested by the pilot. At large airports ATC may coordinate gate operations but this is not technically a clearance, but an instruction of when and where to push. The ground crew may let the pilot know when they can start their engines, but again this would be an instruction.
Taxi will be requested by the pilot, but again ATC will give them instructions, not a clearance. When crossing an active runway, ATC will give an explicit instruction to either cross or hold short of the runway. This is not a clearance but pilots should repeat these instructions back to ATC to help prevent runway incursions.
Upon reaching the runway, especially at a busy airport, the pilots are assumed to be ready. If not they must inform ATC. ATC will then give the pilots their clearance for takeoff. At a less busy airport ATC may wait for the pilots to request clearance. Depending on traffic, ATC may give a "line up and wait" instruction. Then the pilots will be cleared for takeoff.
Once in the air the pilots are expected to fly the route that they were cleared for. Depending on conditions, pilots may request or ATC may offer certain shortcuts or deviations from their route. This could be just a temporary vector. ATC may also clear them to a certain navigation point, but this changes their clearance limit. They are no longer cleared for the rest of the route, only up to where this amended clearance ends. ATC must provide further instructions, which could be as simple as "and then on course".
Changing altitudes are instructions from ATC. ATC will instruct the pilots to climb to the altitude indicated on their flight plan, depending on conditions. Pilots may request altitude changes for weather or performance reasons. Once nearing top of descent, pilots can request descent if ATC hasn't allowed it yet.
Arrival procedures will often require ATC instructions to get the pilots lined up with a runway. ATC will provide them vectors and altitudes. ATC will then clear the pilots to fly an approach to a certain runway. Although pilots may request a certain approach procedure, ATC will decide when to provide the clearance.
Once the aircraft gets closer to the runway, ATC will give clearance to land. The pilots shouldn't have to ask unless they are unsure of their clearance or the tower seems to forget it. If the pilots aren't cleared to land by a certain point, they must follow any missed approach instructions that are given in the approach procedure they were cleared for or by ATC.
Once on the ground, the pilots will receive instructions for taxiing to the gate.