Recently a limitation of 1000 tags was put in place. Some of you may find it hard to believe, but there are communities, that've hit this ceiling long ago (one community I'm moderating had over 6000 tags when this limitation was announced). I've written a small script that helps solve the problem. You give it a list of (probably erroneous) tags to merge, and a tag to merge to, and it replaces all the erroneous tags with the correct one. Here it is:
You will have to create a file with the lists of tags to process. Each line (consisting of coma separated tags) in that file corresponds to a group of tags to merge (with the first one being the one to merge into). For example, if you want to merge all the foo into bar, the file will look like this:
To get the list of options, run the script with -h.