use strict;
use warnings;

#dummy initialization of list of files
#presumably this would be load from a file in real life
#the main thing here is to make sure that the hash is initialized
#so that all values are undefined.
my @aListOfFiles = qw(base1/dir1 base1/dir1/a.png base100/foo.pm);
my %hFound = map { $_ => undef } @aListOfFiles;

my $iLastIndent = 0;
my $iDepth = 0;
my @aPathSegments;
my @aFilePaths;
my %hExtras;


while (my $sLine = <DATA>) {

  #same as grandfather's regex, but
  #(a) strips insignificant trailing whitespace
  #(b) regex for final / is non-capturing
  #    - based on example given by OP, dirs need to be in the
  #      comparison list

  my ($sIndent, $sPathSegment)
    = $sLine =~ m!^(\s*)([^/]*[^\s/])(?:/|\\)?\s*$!;
  next unless defined $sPathSegment and length $sPathSegment;

  #uses jdporter's array idea, but not finicky about number of
  #spaces - only cares whether line is more or less indented
  #than previous line

  #$#dirs = length $indent;
  my $iThisIndent = length $sIndent;
  if ($iLastIndent < $iThisIndent) {
    $iDepth++;
  } elsif ($iLastIndent > $iThisIndent) {
    $iDepth--;
  }
  $iLastIndent=$iThisIndent;
  $aPathSegments[$iDepth] = $sPathSegment;

  my $sFullPath = join('/', @aPathSegments);
  if (exists $hFound{$sFullPath}) {
    #mark path as found
    $hFound{$sFullPath} = 1;
  } else {
    #mark path as extra
    $hExtras{$sFullPath} = 1;
  }
}

print "Missing:\n\t"
  . join("\n\t", grep { ! defined($hFound{$_})} keys %hFound)
  . "\n";
print "Extras:\n\t"
  . join("\n\t", keys %hExtras)
  . "\n";


__DATA__
base1/
 dir1/
    file1.txt
    a.png
 dir2/
 f.txt
base2/
 dir1/
  file1.txt