Merge all text files in a directory and save a temp file
Without going into implementation details, I would suggest looking into the following performance optimisations.


Use buffered reads. If you actually read a line at the time it's pretty time consuming.
Use buffered writes. Instead of writing each new line, collect in a buffer and write in chunks.


For coding review comments, this might be applicable.


The method does 3 different things - merging, syntax checking and bounding rectangle. It might be simpler to maintain and extend the code, if this was refactored into minor helper methods.
Based on the method name, I would be be able to guess what it does.
The initial comments say the method calculates the bounding box, but as the files contain 3d data, would it not be more correct to include the z value.
If the method only need to calculate the bounding rectangle (x,y), is there a need for the merged file to contain the third dimension data ?