you have disabled VLAN4 on the trunk. There is no VLAN4 traffic allowed on the trunk, STP tree for VLAN4 has been disrupted. This is the way how to control spreading of particular VLANs in your network for security or just saving CPU load purposes.
set vtp pruneeligible 4
set vtp pruning enable
you have enabled prunning for VLAN4. This means that VLAN4 user traffic is not sent through the trunk (even VLAN4 broadcasts are not sent) if there is no port assigned to VLAN4 on the downstream switch. The only traffic sent in VLAN4 on the trunk are STP BPDUs, CMP, and similar "Cisco service" protocols.
I think all VLANs are pruneligible but pruning is disabled by default (I'm not 100% sure).
Use sh vtp dom command to see which VLANs are pruneligible and if pruning is enabled.
To your question:
If you configured only
clear trunk 1/1 2-4094
set trunk 1/1 des dot1q 1,2,3
VLAN4 will NOT be added to the trunk automatically.
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