# predeclare subroutines so subs; can be called before being declared
# and without ()
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subroutines don't have to be declared before you can use them in your code. The don't even have to be declared at compile time. If you are using AUTOLOAD the don't even have to defined when the are executed at runtime.
Also, learning the power of regular expressions will make your code more tighty. The following one line could replace your code that follows

# one line to make sure there is one and only one "/"
$target_dir=~s<^/*></>;
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Could replace all this:

#get first character in target_dir
 my $first_char = substr( $target_dir, 0, 1 );

 writeLog( "debug - first character in target_dir $target_dir = $first
+_char" ) if ( $debug );

 if ( $first_char ne '/' ) {
  writeLog( "debug - adding / to beginning of target_dir $target_dir" 
+) if ( $debug );
  #add "/" to beginning of filepath
  $target_dir = '/'.$target_dir;
 }
 else {
  writeLog( "debug - / already exists at beginning. target_dir remains
+ $target_dir" ) if ( $debug );
 }

 #beginning has already been checked for "/" so check for addl
  # "/"s at position 1 ( ///IN/CF/ becomes /IN/CF/ )
 #if position 1 is "/" chop it out and continue until position
  #1 is not a "/"
 writeLog( "debug - checking for multiple '/'s at beginning of target 
+dir $target_dir" ) if ( $debug );
 my $second_char = substr( $target_dir, 1, 1);
 writeLog( "debug - initial second character in target_dir $target_dir
+ = $second_char" ) if ( $debug );
 while ( substr( $target_dir, 1, 1) eq '/' ) {
  writeLog( "debug - removing / from second character in target_dir $t
+arget_dir" ) if ( $debug );
  chop( substr( $target_dir, 1, 1 ) );
  writeLog( "debug - target_dir = $target_dir" ) if ( $debug );
 }
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Also your code has some many comments it makes it hard to read.

#verify that file exists
 checkFileExists() if ( ! $interactive );
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If your function name is almost exactly the same as your comment, you probably don't need the comment