I have moved all of our .htaccess config into <Directory> blocks and set AllowOverride None in the default and default-ssl.

Although after restarting apache it is still reading the .htaccess files. How can I completely turn off reading these files?

Update of all files with "AllowOverride"

/etc/apache2/mods-available/userdir.conf

<IfModule mod_userdir.c>
        UserDir public_html
        UserDir disabled root

        <Directory /home/*/public_html>
                AllowOverride FileInfo AuthConfig Limit Indexes
                Options MultiViews Indexes SymLinksIfOwnerMatch IncludesNoExec
                <Limit GET POST OPTIONS>
                        Order allow,deny
                        Allow from all
                </Limit>
                <LimitExcept GET POST OPTIONS>
                        Order deny,allow
                        Deny from all
                </LimitExcept>
        </Directory>
</IfModule>

/etc/apache2/mods-available/alias.conf

<IfModule alias_module>
#
# Aliases: Add here as many aliases as you need (with no limit). The format is 
# Alias fakename realname
#
# Note that if you include a trailing / on fakename then the server will
# require it to be present in the URL.  So "/icons" isn't aliased in this
# example, only "/icons/".  If the fakename is slash-terminated, then the 
# realname must also be slash terminated, and if the fakename omits the 
# trailing slash, the realname must also omit it.
#
# We include the /icons/ alias for FancyIndexed directory listings.  If
# you do not use FancyIndexing, you may comment this out.
#
Alias /icons/ "/usr/share/apache2/icons/"

<Directory "/usr/share/apache2/icons">
    Options Indexes MultiViews
    AllowOverride None
    Order allow,deny
    Allow from all
</Directory>

</IfModule>

/etc/apache2/httpd.conf

#
# Directives to allow use of AWStats as a CGI
#
Alias /awstatsclasses "/usr/share/doc/awstats/examples/wwwroot/classes/"
Alias /awstatscss "/usr/share/doc/awstats/examples/wwwroot/css/"
Alias /awstatsicons "/usr/share/doc/awstats/examples/wwwroot/icon/"
ScriptAlias /awstats/ "/usr/share/doc/awstats/examples/wwwroot/cgi-bin/"

#
# This is to permit URL access to scripts/files in AWStats directory.
#
<Directory "/usr/share/doc/awstats/examples/wwwroot">
    Options None
    AllowOverride None
    Order allow,deny
    Allow from all
</Directory>

Alias /awstats-icon/ /usr/share/awstats/icon/
<Directory /usr/share/awstats/icon>
Options None
AllowOverride None
Order allow,deny
Allow from all
</Directory>

/etc/apache2/sites-available/default-ssl

<IfModule mod_ssl.c>
<VirtualHost _default_:443>
    ServerAdmin webmaster@localhost

    DocumentRoot /var/www
    <Directory />
        Options FollowSymLinks
        AllowOverride None
    </Directory>
    <Directory /var/www/>
        Options Indexes FollowSymLinks MultiViews
        AllowOverride None
    </Directory>

    ScriptAlias /cgi-bin/ /usr/lib/cgi-bin/
    <Directory "/usr/lib/cgi-bin">
        AllowOverride None
        Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
        Order allow,deny
        Allow from all
    </Directory>

    ErrorLog ${APACHE_LOG_DIR}/error.log

    # Possible values include: debug, info, notice, warn, error, crit,
    # alert, emerg.
    LogLevel warn

    CustomLog ${APACHE_LOG_DIR}/ssl_access.log combined

    #   SSL Engine Switch:
    #   Enable/Disable SSL for this virtual host.
    SSLEngine on

    #   A self-signed (snakeoil) certificate can be created by installing
    #   the ssl-cert package. See
    #   /usr/share/doc/apache2.2-common/README.Debian.gz for more info.
    #   If both key and certificate are stored in the same file, only the
    #   SSLCertificateFile directive is needed.
    SSLCertificateFile    /etc/ssl/certs/ssl-cert-snakeoil.pem
    SSLCertificateKeyFile /etc/ssl/private/ssl-cert-snakeoil.key

    #   Server Certificate Chain:
    #   Point SSLCertificateChainFile at a file containing the
    #   concatenation of PEM encoded CA certificates which form the
    #   certificate chain for the server certificate. Alternatively
    #   the referenced file can be the same as SSLCertificateFile
    #   when the CA certificates are directly appended to the server
    #   certificate for convinience.
    #SSLCertificateChainFile /etc/apache2/ssl.crt/server-ca.crt

    #   Certificate Authority (CA):
    #   Set the CA certificate verification path where to find CA
    #   certificates for client authentication or alternatively one
    #   huge file containing all of them (file must be PEM encoded)
    #   Note: Inside SSLCACertificatePath you need hash symlinks
    #         to point to the certificate files. Use the provided
    #         Makefile to update the hash symlinks after changes.
    #SSLCACertificatePath /etc/ssl/certs/
    #SSLCACertificateFile /etc/apache2/ssl.crt/ca-bundle.crt

    #   Certificate Revocation Lists (CRL):
    #   Set the CA revocation path where to find CA CRLs for client
    #   authentication or alternatively one huge file containing all
    #   of them (file must be PEM encoded)
    #   Note: Inside SSLCARevocationPath you need hash symlinks
    #         to point to the certificate files. Use the provided
    #         Makefile to update the hash symlinks after changes.
    #SSLCARevocationPath /etc/apache2/ssl.crl/
    #SSLCARevocationFile /etc/apache2/ssl.crl/ca-bundle.crl

    #   Client Authentication (Type):
    #   Client certificate verification type and depth.  Types are
    #   none, optional, require and optional_no_ca.  Depth is a
    #   number which specifies how deeply to verify the certificate
    #   issuer chain before deciding the certificate is not valid.
    #SSLVerifyClient require
    #SSLVerifyDepth  10

    #   Access Control:
    #   With SSLRequire you can do per-directory access control based
    #   on arbitrary complex boolean expressions containing server
    #   variable checks and other lookup directives.  The syntax is a
    #   mixture between C and Perl.  See the mod_ssl documentation
    #   for more details.
    #<Location />
    #SSLRequire (    %{SSL_CIPHER} !~ m/^(EXP|NULL)/ \
    #            and %{SSL_CLIENT_S_DN_O} eq "Snake Oil, Ltd." \
    #            and %{SSL_CLIENT_S_DN_OU} in {"Staff", "CA", "Dev"} \
    #            and %{TIME_WDAY} >= 1 and %{TIME_WDAY} <= 5 \
    #            and %{TIME_HOUR} >= 8 and %{TIME_HOUR} <= 20       ) \
    #           or %{REMOTE_ADDR} =~ m/^192\.76\.162\.[0-9]+$/
    #</Location>

    #   SSL Engine Options:
    #   Set various options for the SSL engine.
    #   o FakeBasicAuth:
    #     Translate the client X.509 into a Basic Authorisation.  This means that
    #     the standard Auth/DBMAuth methods can be used for access control.  The
    #     user name is the `one line' version of the client's X.509 certificate.
    #     Note that no password is obtained from the user. Every entry in the user
    #     file needs this password: `xxj31ZMTZzkVA'.
    #   o ExportCertData:
    #     This exports two additional environment variables: SSL_CLIENT_CERT and
    #     SSL_SERVER_CERT. These contain the PEM-encoded certificates of the
    #     server (always existing) and the client (only existing when client
    #     authentication is used). This can be used to import the certificates
    #     into CGI scripts.
    #   o StdEnvVars:
    #     This exports the standard SSL/TLS related `SSL_*' environment variables.
    #     Per default this exportation is switched off for performance reasons,
    #     because the extraction step is an expensive operation and is usually
    #     useless for serving static content. So one usually enables the
    #     exportation for CGI and SSI requests only.
    #   o StrictRequire:
    #     This denies access when "SSLRequireSSL" or "SSLRequire" applied even
    #     under a "Satisfy any" situation, i.e. when it applies access is denied
    #     and no other module can change it.
    #   o OptRenegotiate:
    #     This enables optimized SSL connection renegotiation handling when SSL
    #     directives are used in per-directory context.
    #SSLOptions +FakeBasicAuth +ExportCertData +StrictRequire
    <FilesMatch "\.(cgi|shtml|phtml|php)$">
        SSLOptions +StdEnvVars
    </FilesMatch>
    <Directory /usr/lib/cgi-bin>
        SSLOptions +StdEnvVars
    </Directory>

    #   SSL Protocol Adjustments:
    #   The safe and default but still SSL/TLS standard compliant shutdown
    #   approach is that mod_ssl sends the close notify alert but doesn't wait for
    #   the close notify alert from client. When you need a different shutdown
    #   approach you can use one of the following variables:
    #   o ssl-unclean-shutdown:
    #     This forces an unclean shutdown when the connection is closed, i.e. no
    #     SSL close notify alert is send or allowed to received.  This violates
    #     the SSL/TLS standard but is needed for some brain-dead browsers. Use
    #     this when you receive I/O errors because of the standard approach where
    #     mod_ssl sends the close notify alert.
    #   o ssl-accurate-shutdown:
    #     This forces an accurate shutdown when the connection is closed, i.e. a
    #     SSL close notify alert is send and mod_ssl waits for the close notify
    #     alert of the client. This is 100% SSL/TLS standard compliant, but in
    #     practice often causes hanging connections with brain-dead browsers. Use
    #     this only for browsers where you know that their SSL implementation
    #     works correctly.
    #   Notice: Most problems of broken clients are also related to the HTTP
    #   keep-alive facility, so you usually additionally want to disable
    #   keep-alive for those clients, too. Use variable "nokeepalive" for this.
    #   Similarly, one has to force some clients to use HTTP/1.0 to workaround
    #   their broken HTTP/1.1 implementation. Use variables "downgrade-1.0" and
    #   "force-response-1.0" for this.
    BrowserMatch "MSIE [2-6]" \
        nokeepalive ssl-unclean-shutdown \
        downgrade-1.0 force-response-1.0
    # MSIE 7 and newer should be able to use keepalive
    BrowserMatch "MSIE [17-9]" ssl-unclean-shutdown

</VirtualHost>
</IfModule>

/etc/apache2/sites-available/default

<VirtualHost *:80>
    ServerAdmin webmaster@localhost

    DocumentRoot /var/www
    <Directory />
        Options FollowSymLinks
        AllowOverride None
    </Directory>

    <Directory /var/www/>
        Options -Indexes FollowSymLinks MultiViews
        AllowOverride None
        Order allow,deny
        allow from all
    </Directory>

    ScriptAlias /cgi-bin/ /usr/lib/cgi-bin/
    <Directory "/usr/lib/cgi-bin">
        AllowOverride None
        Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
        Order allow,deny
        Allow from all
    </Directory>


    Alias /delboy /usr/share/phpmyadmin
    <Directory /usr/share/phpmyadmin>
        # Restrict phpmyadmin access
        Order Deny,Allow
        Allow from all
    </Directory>

    ErrorLog ${APACHE_LOG_DIR}/error.log

    # Possible values include: debug, info, notice, warn, error, crit,
    # alert, emerg.
    LogLevel warn

    CustomLog ${APACHE_LOG_DIR}/access.log combined

    Alias /doc/ "/usr/share/doc/"
    <Directory "/usr/share/doc/">
        Options Indexes MultiViews FollowSymLinks
        AllowOverride None
        Order deny,allow
        Deny from all
        Allow from 127.0.0.0/255.0.0.0 ::1/128
    </Directory>

</VirtualHost>

/etc/apache2/conf.d/security

#
# Disable access to the entire file system except for the directories that
# are explicitly allowed later.
#
# This currently breaks the configurations that come with some web application
# Debian packages.
#
#<Directory />
#   AllowOverride None
#   Order Deny,Allow
#   Deny from all
#</Directory>


# Changing the following options will not really affect the security of the
# server, but might make attacks slightly more difficult in some cases.

#
# ServerTokens
# This directive configures what you return as the Server HTTP response
# Header. The default is 'Full' which sends information about the OS-Type
# and compiled in modules.
# Set to one of:  Full | OS | Minimal | Minor | Major | Prod
# where Full conveys the most information, and Prod the least.
#
#ServerTokens Minimal
ServerTokens OS
#ServerTokens Full

#
# Optionally add a line containing the server version and virtual host
# name to server-generated pages (internal error documents, FTP directory
# listings, mod_status and mod_info output etc., but not CGI generated
# documents or custom error documents).
# Set to "EMail" to also include a mailto: link to the ServerAdmin.
# Set to one of:  On | Off | EMail
#
#ServerSignature Off
ServerSignature On

#
# Allow TRACE method
#
# Set to "extended" to also reflect the request body (only for testing and
# diagnostic purposes).
#
# Set to one of:  On | Off | extended
#
TraceEnable Off
#TraceEnable On

/etc/apache2/apache2.conf

#
# Based upon the NCSA server configuration files originally by Rob McCool.
#
# This is the main Apache server configuration file.  It contains the
# configuration directives that give the server its instructions.
# See http://httpd.apache.org/docs/2.2/ for detailed information about
# the directives.
#
# Do NOT simply read the instructions in here without understanding
# what they do.  They're here only as hints or reminders.  If you are unsure
# consult the online docs. You have been warned.  
#
# The configuration directives are grouped into three basic sections:
#  1. Directives that control the operation of the Apache server process as a
#     whole (the 'global environment').
#  2. Directives that define the parameters of the 'main' or 'default' server,
#     which responds to requests that aren't handled by a virtual host.
#     These directives also provide default values for the settings
#     of all virtual hosts.
#  3. Settings for virtual hosts, which allow Web requests to be sent to
#     different IP addresses or hostnames and have them handled by the
#     same Apache server process.
#
# Configuration and logfile names: If the filenames you specify for many
# of the server's control files begin with "/" (or "drive:/" for Win32), the
# server will use that explicit path.  If the filenames do *not* begin
# with "/", the value of ServerRoot is prepended -- so "foo.log"
# with ServerRoot set to "/etc/apache2" will be interpreted by the
# server as "/etc/apache2/foo.log".
#

### Section 1: Global Environment
#
# The directives in this section affect the overall operation of Apache,
# such as the number of concurrent requests it can handle or where it
# can find its configuration files.
#

#
# ServerRoot: The top of the directory tree under which the server's
# configuration, error, and log files are kept.
#
# NOTE!  If you intend to place this on an NFS (or otherwise network)
# mounted filesystem then please read the LockFile documentation (available
# at <URL:http://httpd.apache.org/docs/2.2/mod/mpm_common.html#lockfile>);
# you will save yourself a lot of trouble.
#
# Do NOT add a slash at the end of the directory path.
#
#ServerRoot "/etc/apache2"

#
# The accept serialization lock file MUST BE STORED ON A LOCAL DISK.
#
LockFile ${APACHE_LOCK_DIR}/accept.lock

#
# PidFile: The file in which the server should record its process
# identification number when it starts.
# This needs to be set in /etc/apache2/envvars
#
PidFile ${APACHE_PID_FILE}

#
# Timeout: The number of seconds before receives and sends time out.
#
Timeout 300

#
# KeepAlive: Whether or not to allow persistent connections (more than
# one request per connection). Set to "Off" to deactivate.
#
KeepAlive On

#
# MaxKeepAliveRequests: The maximum number of requests to allow
# during a persistent connection. Set to 0 to allow an unlimited amount.
# We recommend you leave this number high, for maximum performance.
#
MaxKeepAliveRequests 100

#
# KeepAliveTimeout: Number of seconds to wait for the next request from the
# same client on the same connection.
#
KeepAliveTimeout 4

##
## Server-Pool Size Regulation (MPM specific)
## 

# prefork MPM
# StartServers: number of server processes to start
# MinSpareServers: minimum number of server processes which are kept spare
# MaxSpareServers: maximum number of server processes which are kept spare
# MaxClients: maximum number of server processes allowed to start
# MaxRequestsPerChild: maximum number of requests a server process serves
<IfModule mpm_prefork_module>
    StartServers          5
    MinSpareServers       5
    MaxSpareServers      10
    MaxClients          150
    MaxRequestsPerChild  500
</IfModule>

# worker MPM
# StartServers: initial number of server processes to start
# MaxClients: maximum number of simultaneous client connections
# MinSpareThreads: minimum number of worker threads which are kept spare
# MaxSpareThreads: maximum number of worker threads which are kept spare
# ThreadLimit: ThreadsPerChild can be changed to this maximum value during a
#              graceful restart. ThreadLimit can only be changed by stopping
#              and starting Apache.
# ThreadsPerChild: constant number of worker threads in each server process
# MaxRequestsPerChild: maximum number of requests a server process serves
<IfModule mpm_worker_module>
    StartServers          2
    MinSpareThreads      25
    MaxSpareThreads      75 
    ThreadLimit          64
    ThreadsPerChild      25
    MaxClients          150
    MaxRequestsPerChild   0
</IfModule>

# event MPM
# StartServers: initial number of server processes to start
# MaxClients: maximum number of simultaneous client connections
# MinSpareThreads: minimum number of worker threads which are kept spare
# MaxSpareThreads: maximum number of worker threads which are kept spare
# ThreadsPerChild: constant number of worker threads in each server process
# MaxRequestsPerChild: maximum number of requests a server process serves
<IfModule mpm_event_module>
    StartServers          2
    MaxClients          150
    MinSpareThreads      25
    MaxSpareThreads      75 
    ThreadLimit          64
    ThreadsPerChild      25
    MaxRequestsPerChild   0
</IfModule>

# These need to be set in /etc/apache2/envvars
User ${APACHE_RUN_USER}
Group ${APACHE_RUN_GROUP}

#
# AccessFileName: The name of the file to look for in each directory
# for additional configuration directives.  See also the AllowOverride
# directive.
#

AccessFileName .htaccess

#
# The following lines prevent .htaccess and .htpasswd files from being 
# viewed by Web clients. 
#
<Files ~ "^\.ht">
    Order allow,deny
    Deny from all
    Satisfy all
</Files>

#
# DefaultType is the default MIME type the server will use for a document
# if it cannot otherwise determine one, such as from filename extensions.
# If your server contains mostly text or HTML documents, "text/plain" is
# a good value.  If most of your content is binary, such as applications
# or images, you may want to use "application/octet-stream" instead to
# keep browsers from trying to display binary files as though they are
# text.
#
DefaultType text/plain


#
# HostnameLookups: Log the names of clients or just their IP addresses
# e.g., www.apache.org (on) or 204.62.129.132 (off).
# The default is off because it'd be overall better for the net if people
# had to knowingly turn this feature on, since enabling it means that
# each client request will result in AT LEAST one lookup request to the
# nameserver.
#
HostnameLookups Off

# ErrorLog: The location of the error log file.
# If you do not specify an ErrorLog directive within a <VirtualHost>
# container, error messages relating to that virtual host will be
# logged here.  If you *do* define an error logfile for a <VirtualHost>
# container, that host's errors will be logged there and not here.
#
ErrorLog ${APACHE_LOG_DIR}/error.log

#
# LogLevel: Control the number of messages logged to the error_log.
# Possible values include: debug, info, notice, warn, error, crit,
# alert, emerg.
#
LogLevel warn

# Include module configuration:
Include mods-enabled/*.load
Include mods-enabled/*.conf

# Include all the user configurations:
Include httpd.conf

# Include ports listing
Include ports.conf

#
# The following directives define some format nicknames for use with
# a CustomLog directive (see below).
# If you are behind a reverse proxy, you might want to change %h into %{X-Forwarded-For}i
#
LogFormat "%v:%p %h %l %u %t \"%r\" %>s %O \"%{Referer}i\" \"%{User-Agent}i\"" vhost_combined
LogFormat "%h %l %u %t \"%r\" %>s %O \"%{Referer}i\" \"%{User-Agent}i\"" combined
LogFormat "%h %l %u %t \"%r\" %>s %O" common
LogFormat "%{Referer}i -> %U" referer
LogFormat "%{User-agent}i" agent

# Include of directories ignores editors' and dpkg's backup files,
# see README.Debian for details.

# Include generic snippets of statements
Include conf.d/

# Include the virtual host configurations:
Include sites-enabled/