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Then I wrote a custom script that is copied to my home directory on the Rpi, which can be obtained here (I recommend using Chromium on the Rpi to get and save it):

 http://calttc.net/AMS2Rpi

Then I set it to executable and run it:

Then I wrote a custom script that is copied to my home directory on the Rpi, which can be obtained here as a text file (use Chromium or wget to copy it to the file ~/AMS2Rpi) - Here is the link:  http://calttc.net/AMS2Rpi

Then set it to executable and run it:

#! /bin/bash
#
#  AMS2Rpi - Converts MS Arduino IDE Sketch names to RPI Arduino IDE Sketch names
#
#                  SDsolar      2017-01-29
#
#  Reason:    Arduino IDE on MS inserts underscore characters in file & directory names
#             Arduino IDE on Rpi rejects all but alphanumeric characters
#
#  Solution:  Remove all but alphanumeric characters 
#             and capitalize each word in the names
#
#  Usage:  
#    Install Raspbian Arduino IDE 2:1.0.5 on the Raspberry Pi 3
#    Use a USB flash drive to copy sketches and libraries from the MS-based Arduino IDE
#      On the Rpi, copy the libraries directory to ~/sketchbook/libraries
#      On the Rpi, copy the sketches directory to ~sketchbook/AMSsketches
#    Copy this script to your home directory as AMS2Rpi using Chromium
#    cd
#    chmod +x AMS2Rpi
#    ./AMS2Rpi    (This will take some time)
#    cat /tmp/AMS2Rpi | grep "AMSsketches" >~/AMSRpiQ
#    chmod +x ~/AMS2RpiQ
#    ~/AMS2RpiQ
#    Open the Rpi Arduino IDE 
#
#  Alternatively, if you have a lot of sketches you might want to
#    change the "mv -i" below to "mv" 
#    and cat it into AM2SRpiX above
#    so you don't need to answer "y" for every rename.
#
#  Props to Marco Fioretti for his article at http://www.techrepublic.com/blog/linux-and-open-source/how-to-remove-weird-characters-from-file-and-directory-names-automatically/
# ---------------------------------------------------------------------
rm -f /tmp/AMS2R*
cd $1
find .  | awk '{ print length(), $0 | "sort -n -r" }' | \
        grep -v '^1 \.$' | cut -d/ -f2- > /tmp/AMS2Rpi_1
touch /tmp/AMS2Rpi_2
while read line
  do
  BASE=`basename "$line"`
  NEWBASE=`basename "$line" | perl -e '$N = <>; chomp ($N); $N =~ s/[^a-zA-Z0-9.]//g; $N =~ s/_+/_/g; $N= lc($N); $N =~ s/_([a-z])/_.uc($1)/eg; print ucfirst($N);' `
  if [ "$BASE" != "$NEWBASE" ]
  then
  OLDPATH=$(echo "$line" | sed -r 's/([^a-zA-Z0-9./_-])/\\\1/g')
  DIR=$(dirname "$line" | sed -r 's/([^a-zA-Z0-9./_-])/\\\1/g')
  echo "mv -i $OLDPATH $DIR/$NEWBASE" >> /tmp/AMS2Rpi_2
  fi
done </tmp/AMS2Rpi_1
rm -f /tmp/AMS2Rpi_1
mv /tmp/AMS2Rpi_2 /tmp/AMS2RPi
exit

#! /bin/bash
#
#  AMS2Rpi - Converts MS Arduino IDE Sketch names to RPI Arduino IDE Sketch names
#
#                  SDsolar      2017-01-29
#
#  Reason:    Arduino IDE on MS inserts underscore characters in file & directory names
#             Arduino IDE on Rpi rejects all but alphanumeric characters
#
#  Solution:  Remove all but alphanumeric characters 
#             and capitalize each word in the names
#
#  Usage:  
#    Install Raspbian Arduino IDE 2:1.0.5 on the Raspberry Pi 3
#    Use a USB flash drive to copy sketches and libraries from the MS-based Arduino IDE
#      On the Rpi, copy the libraries directory to ~/sketchbook/libraries
#      On the Rpi, copy the sketches directory to ~sketchbook/AMSsketches
#    Copy this script to your home directory as AMS2Rpi using Chromium
#    cd
#    chmod +x AMS2Rpi
#    ./AMS2Rpi    (This will take some time)
#    cat /tmp/AMS2Rpi | grep "AMSsketches" >~/AMSRpiQ
#    chmod +x ~/AMS2RpiQ
#    ~/AMS2RpiQ
#    Open the Rpi Arduino IDE 
#
#  Alternatively, if you have a lot of sketches you might want to
#    change the "mv -i" below to "mv" 
#    and cat it into AM2SRpiX above
#    so you don't need to answer "y" for every rename.
#
#  Props to Marco Fioretti for his article at http://www.techrepublic.com/blog/linux-and-open-source/how-to-remove-weird-characters-from-file-and-directory-names-automatically/
# ---------------------------------------------------------------------
rm -f /tmp/AMS2R*
cd $1
find .  | awk '{ print length(), $0 | "sort -n -r" }' | \
        grep -v '^1 \.$' | cut -d/ -f2- > /tmp/AMS2Rpi_1
touch /tmp/AMS2Rpi_2
while read line
  do
  BASE=`basename "$line"`
  NEWBASE=`basename "$line" | perl -e '$N = <>; chomp ($N); $N =~ s/[^a-zA-Z0-9.]//g; $N =~ s/_+/_/g; $N= lc($N); $N =~ s/_([a-z])/_.uc($1)/eg; print ucfirst($N);' `
  if [ "$BASE" != "$NEWBASE" ]
  then
  OLDPATH=$(echo "$line" | sed -r 's/([^a-zA-Z0-9./_-])/\\\1/g')
  DIR=$(dirname "$line" | sed -r 's/([^a-zA-Z0-9./_-])/\\\1/g')
  echo "mv -i $OLDPATH $DIR/$NEWBASE" >> /tmp/AMS2Rpi_2
  fi
done </tmp/AMS2Rpi_1
rm -f /tmp/AMS2Rpi_1
mv /tmp/AMS2Rpi_2 /tmp/AMS2Rpi
exit

cat /tmp/AMS2RpiQ | grep "AMSsketches" >~/AMS2RpiQ

cat /tmp/AMS2Rpi | grep "AMSsketches" >~/AMS2RpiQ