The following python script should do what you want. Just copy the contents in a file (named sc1.py, say) in the folder which contains all the subfolders you want to merge. Then run the command chmod +x sc1.py and then run this file in that folder ./sc1.py and you should get the result. What this script will do is the following:
Say you are working in the folder /home/bob/foo and you have hundreds of folders bar1, bar2,....,bar99 inside the folder foo.
Run the script in /home/bob/foo/ and it will create a folder /home/bob/foo/Merged and it will transfer the contents of all the folders bar1,bar2 etc... inside the folder Merged. The directory stuctures inside the folders bar1,bar2 etc will remain intact
You may want to test this somewhere to see that this is what you asked for.
#!/usr/bin/env python
import subprocess as sbp
import os
path=os.getcwd()
fol = os.listdir(path)
p2 = os.path.join(path,'Merged')
sbp.Popen(['mkdir','Merged'])
for i in fol:
if os.path.isdir(i)==True:
if i!='Merged':
p1 = os.path.join(path,i)
p3 = 'cp -r "' + p1 +'"/* ' + p2
sbp.Popen(p3,shell=True)
Note: I am an absolute beginner at scripting and just learned most of these commands. If there are suggestions to improve from the folks around - greatly appreciated.