Website on shared hosting with pi-hole is blocked

[Myroslav_Galavai]

Expected Behaviour:

My own website (same server with pi-hole) shouldn't be blocked

Actual Behaviour:

Actually it is. Whitelisting the domain doesn't help

Update: after some research I think the issue is in conflict of pi-hole and my current webserver (apache).
Tried to apply found fixes, but it didn't worked for me. Please help.
Broken link sample:
http://bebinka.com/nooks-and-crannies/

Debug Token:

6cmqa3jos5

[jacob.salmela]

Your Pi-hole is an open resolver. You should fix that before doing anything else.

[Myroslav_Galavai]

Thanks. I think, I fixed this just now.
But the main problem is still there.

[Mcat12]

Make sure that each web server has its own port. You should really not be running Pi-hole on the same machine as your web site.

[jacob.salmela]

@Myroslav_Galavai

But the main problem is still there.

We've had some whitelisting issues with this release. Have you looked at this post?

[PSA] Having Whitelisting issues with 3.3? Read here

Hi All, After a few days of pulling out our hair and troubleshooting this whitelisting issue that some of you have reported, we're finally getting to the bottom of it. The good news is, whitelisting is not completely broken. You can still whitelist domains from the cli with no issues by calling pihole -w [domain-to-whitelist]. The issue only affects whitelisting from the admin page (whitelist page, query log, and block page) Take a look over this pull request where I've attempted to explain w…

[Myroslav_Galavai]

I'm on version 3.3 from the start.

[Myroslav_Galavai]

I tried to uninstall the pi-hole correctly, this renders all the previously blocked folders as 404..
How to fix..? It's a basic WP installation on Apache and Ubuntu.

[Myroslav_Galavai]

Guys, it seems to me I dig down to the root of my issue – pi-hole replaced the lighttpd.conf, that's why all the sub-dirs of my website except the / are returning 404 error.
How to fix this?
cat /etc/lighttpd/lighttpd.conf
# Pi-hole: A black hole for Internet advertisements
# (c) 2017 Pi-hole, LLC (https://pi-hole.net)
# Network-wide ad blocking via your own hardware.
#
# Lighttpd config for Pi-hole
#
# This file is copyright under the latest version of the EUPL.
# Please see LICENSE file for your rights under this license.

###############################################################################
#     FILE AUTOMATICALLY OVERWRITTEN BY PI-HOLE INSTALL/UPDATE PROCEDURE.     #
# ANY CHANGES MADE TO THIS FILE AFTER INSTALL WILL BE LOST ON THE NEXT UPDATE #
#                                                                             #
#              CHANGES SHOULD BE MADE IN A SEPARATE CONFIG FILE:              #
#                         /etc/lighttpd/external.conf                         #
###############################################################################

server.modules = (
	"mod_access",
	"mod_accesslog",
	"mod_auth",
	"mod_expire",
	"mod_compress",
	"mod_redirect",
	"mod_setenv",
	"mod_rewrite"
)

server.document-root        = "/var/www/html"
server.error-handler-404    = "pihole/index.php"
server.upload-dirs          = ( "/var/cache/lighttpd/uploads" )
server.errorlog             = "/var/log/lighttpd/error.log"
server.pid-file             = "/var/run/lighttpd.pid"
server.username             = "www-data"
server.groupname            = "www-data"
server.port                 = 80
accesslog.filename          = "/var/log/lighttpd/access.log"
accesslog.format            = "%{%s}t|%V|%r|%s|%b"

index-file.names            = ( "index.php", "index.html", "index.lighttpd.html" )
url.access-deny             = ( "~", ".inc", ".md", ".yml", ".ini" )
static-file.exclude-extensions = ( ".php", ".pl", ".fcgi" )

compress.cache-dir          = "/var/cache/lighttpd/compress/"
compress.filetype           = ( "application/javascript", "text/css", "text/html", "text/plain" )

# default listening port for IPv6 falls back to the IPv4 port
include_shell "/usr/share/lighttpd/use-ipv6.pl " + server.port
include_shell "/usr/share/lighttpd/create-mime.assign.pl"

# Prevent Lighttpd from enabling Let's Encrypt SSL for every blocked domain
#include_shell "/usr/share/lighttpd/include-conf-enabled.pl"
include_shell "find /etc/lighttpd/conf-enabled -name '*.conf' -a ! -name 'letsencrypt.conf' -printf 'include \"%p\"\n' 2>/dev/null"

# If the URL starts with /admin, it is the Web interface
$HTTP["url"] =~ "^/admin/" {
    # Create a response header for debugging using curl -I
    setenv.add-response-header = (
        "X-Pi-hole" => "The Pi-hole Web interface is working!",
        "X-Frame-Options" => "DENY"
    )

    $HTTP["url"] =~ ".ttf$" {
        # Allow Block Page access to local fonts
        setenv.add-response-header = ( "Access-Control-Allow-Origin" => "*" )
    }
}

# Block . files from being served, such as .git, .github, .gitignore
$HTTP["url"] =~ "^/admin/\.(.*)" {
     url.access-deny = ("")
}

# Add user chosen options held in external file
include_shell "cat external.conf 2>/dev/null"

[jacob.salmela]

@Myroslav_Galavai

# Add user chosen options held in external file
include_shell "cat external.conf 2>/dev/null"

If you create the external.conf file, you can set additional lighttpd directives.