#!/usr/bin/env perl -l

use strict;
use warnings;

get_clean_ini_data();

for (qw{MySection AnotherSection WhitespaceSection}) {
    print "Contents of '$_':\n", get_section($_);
}

{
    my %section_lines_for;

    sub get_clean_ini_data {
        my $current_section;

        while (<DATA>) {
            s/^\s*(.*?)\s*$/$1/;
            next unless length;

            if (/^\[([^]]+)/) {
                my $new_section = $1;
                strip_trailing_comments($current_section);
                $current_section = $new_section;
            }
            else {
                push @{$section_lines_for{$current_section}}, $_;
            }
        }

        strip_trailing_comments($current_section);
    }

    sub strip_trailing_comments {
        my $section = shift;

        return unless defined $section;

        for my $i (reverse 0 ..  $#{$section_lines_for{$section}}) {
            if (0 == index $section_lines_for{$section}[$i], ';') {
                pop @{$section_lines_for{$section}};
            }
            else {
                last;
            }
        }
    }

    sub get_section { join "\n", @{$section_lines_for{$_[0]}} }
}

__DATA__
[MySection]
; This is a comment line for MySection
fld1 = 'value of field 1' 
fld2 = 42

; This is the heading for AnotherSection
[AnotherSection]
; another comment
asfld=69

 ; Heading for WhitespaceSection
[WhitespaceSection]
    ; Comment starting with a tab
     ; Comment starting with a tab and a space
 ; Comment starting with a space
; Comment ending with a tab 
; Comment ending with a tab and a space  
; Comment ending with a space 
     ; tab+space+comment+space+tab  
    ; space+tab+comment+tab+space    

qwe=rty
asd=fgh
; trailing 1
    ; tab + trailing 2
 ; space + trailing 3
; trailing 4

##</code><code>##

$ pm_1178405_ini_file_clean.pl
Contents of 'MySection':
; This is a comment line for MySection
fld1 = 'value of field 1'
fld2 = 42
Contents of 'AnotherSection':
; another comment
asfld=69
Contents of 'WhitespaceSection':
; Comment starting with a tab
; Comment starting with a tab and a space
; Comment starting with a space
; Comment ending with a tab
; Comment ending with a tab and a space
; Comment ending with a space
; tab+space+comment+space+tab
; space+tab+comment+tab+space
qwe=rty
asd=fgh

##</code><code>##

$ cat -vet pm_1178405_ini_file_clean.pl
...
__DATA__$
[MySection]$
; This is a comment line for MySection$
fld1 = 'value of field 1' $
fld2 = 42$
$
; This is the heading for AnotherSection$
[AnotherSection]$
; another comment$
asfld=69$
$
 ; Heading for WhitespaceSection$
[WhitespaceSection]$
^I; Comment starting with a tab$
^I ; Comment starting with a tab and a space$
 ; Comment starting with a space$
; Comment ending with a tab^I$
; Comment ending with a tab and a space^I $
; Comment ending with a space $
^I ; tab+space+comment+space+tab ^I$
 ^I; space+tab+comment+tab+space^I $
$
qwe=rty$
asd=fgh$
; trailing 1$
^I; tab + trailing 2$
 ; space + trailing 3$
; trailing 4$

##</code><code>##

$ pm_1178405_ini_file_clean.pl | cat -vet
Contents of 'MySection':$
; This is a comment line for MySection$
fld1 = 'value of field 1'$
fld2 = 42$
Contents of 'AnotherSection':$
; another comment$
asfld=69$
Contents of 'WhitespaceSection':$
; Comment starting with a tab$
; Comment starting with a tab and a space$
; Comment starting with a space$
; Comment ending with a tab$
; Comment ending with a tab and a space$
; Comment ending with a space$
; tab+space+comment+space+tab$
; space+tab+comment+tab+space$
qwe=rty$
asd=fgh$