I did run the 'bless' command (as given in the Guide and with 'sudo') right after point 6 of the Chameleon installation. I've tried the 'bless' command again with double dashes for the options (as seen in the man pages) - same result, it still boots Windows automatically on the Bootcamp partition.
How can I change / swap the Boot priority between disk0 (internal SSD of the MBP) and disk1 (external SSD for Yosemite)?
You can't change what the disk identifier is and it will sometimes change by itself. The only way to get around it is to put Clover/Chameleon on the same HDD as Windows in the first partition. For example, my current setup is a single HDD with partitions in this order Mavericks/Clover/Win7 and Yosemite on another HDD. Before I had Clover on a second drive with Yosemite but if I wanted to boot Clover I had to pull my Mavericks/Win7 drive. To boot Mavericks with clover you have to remove the Tiamo boot.efi files and put back the originals.
If Clover and Windows are on the same drive you will also have to set the Clover/Chameleon partition as the active partition. This can be done using diskpart in Windows or fdisk in OS X.
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Clover is no go - no bootable disk found.
Restored Clover and it is working with all disks installed. But no iMessage...
The no bootable disk found with Clover on a GPT normally means that there isn't a hybrid MBR present.