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Cloud Flare honestly does not do alot. it actually causes more issues than anything. Really it depends on how your host setup your cpanel through whm. Many of them do really do a minimum which leaves alot of vulnerabilities (ports open that don't need to be, extra processes, insecure application configs for mysql, php etc...). The list is long of possibilities on a standard cpanel install. If you don't have root or WHM access than you will need to work with your host.

Start by doing a search of your http logs for these 2 words htaccess and filemanager
and see if you find any.

X vBulletin 3.8.12 by vBS Debug Information
Template Usage: (1)SHOWTHREAD_SHOWPOST (1)ad_footer_end (1)ad_footer_start (1)ad_header_end (1)ad_header_logo (1)ad_navbar_below (1)footer (1)gobutton (1)header (1)headinclude (6)option (1)post_thanks_box (1)post_thanks_button (1)post_thanks_javascript (1)post_thanks_navbar_search (1)post_thanks_postbit_info (1)postbit (1)postbit_onlinestatus (1)postbit_wrapper (1)spacer_close (1)spacer_open Phrase Groups Available: global postbit reputationlevel showthread	Included Files: ./showpost.php ./global.php ./includes/init.php ./includes/class_core.php ./includes/config.php ./includes/functions.php ./includes/class_hook.php ./includes/modsystem_functions.php ./includes/functions_bigthree.php ./includes/class_postbit.php ./includes/class_bbcode.php ./includes/functions_reputation.php ./includes/functions_post_thanks.php Hooks Called: init_startup init_startup_session_setup_start init_startup_session_setup_complete cache_permissions fetch_postinfo_query fetch_postinfo fetch_threadinfo_query fetch_threadinfo fetch_foruminfo style_fetch cache_templates global_start parse_templates global_setup_complete showpost_start bbcode_fetch_tags bbcode_create postbit_factory showpost_post postbit_display_start post_thanks_function_post_thanks_off_start post_thanks_function_post_thanks_off_end post_thanks_function_fetch_thanks_start post_thanks_function_fetch_thanks_end post_thanks_function_thanked_already_start post_thanks_function_thanked_already_end fetch_musername postbit_imicons bbcode_parse_start bbcode_parse_complete_precache bbcode_parse_complete postbit_display_complete post_thanks_function_can_thank_this_post_start showpost_complete
Messages:

X vBulletin 3.8.12 by vBS Debug Information

Page Generation 0.01288 seconds
Memory Usage 1,754KB
Queries Executed 11 (?)

More Information

Template Usage:

(1)SHOWTHREAD_SHOWPOST
(1)ad_footer_end
(1)ad_footer_start
(1)ad_header_end
(1)ad_header_logo
(1)ad_navbar_below
(1)footer
(1)gobutton
(1)header
(1)headinclude
(6)option
(1)post_thanks_box
(1)post_thanks_button
(1)post_thanks_javascript
(1)post_thanks_navbar_search
(1)post_thanks_postbit_info
(1)postbit
(1)postbit_onlinestatus
(1)postbit_wrapper
(1)spacer_close
(1)spacer_open

Phrase Groups Available:

global
postbit
reputationlevel
showthread

Included Files:

./showpost.php
./global.php
./includes/init.php
./includes/class_core.php
./includes/config.php
./includes/functions.php
./includes/class_hook.php
./includes/modsystem_functions.php
./includes/functions_bigthree.php
./includes/class_postbit.php
./includes/class_bbcode.php
./includes/functions_reputation.php
./includes/functions_post_thanks.php

Hooks Called:

init_startup
init_startup_session_setup_start
init_startup_session_setup_complete
cache_permissions
fetch_postinfo_query
fetch_postinfo
fetch_threadinfo_query
fetch_threadinfo
fetch_foruminfo
style_fetch
cache_templates
global_start
parse_templates
global_setup_complete
showpost_start
bbcode_fetch_tags
bbcode_create
postbit_factory
showpost_post
postbit_display_start
post_thanks_function_post_thanks_off_start
post_thanks_function_post_thanks_off_end
post_thanks_function_fetch_thanks_start
post_thanks_function_fetch_thanks_end
post_thanks_function_thanked_already_start
post_thanks_function_thanked_already_end
fetch_musername
postbit_imicons
bbcode_parse_start
bbcode_parse_complete_precache
bbcode_parse_complete
postbit_display_complete
post_thanks_function_can_thank_this_post_start
showpost_complete

Messages:

X vBulletin 3.8.12 by vBS Debug Information
Page Generation 0.01288 seconds Memory Usage 1,754KB Queries Executed 11 (?)
More Information
Template Usage: (1)SHOWTHREAD_SHOWPOST (1)ad_footer_end (1)ad_footer_start (1)ad_header_end (1)ad_header_logo (1)ad_navbar_below (1)footer (1)gobutton (1)header (1)headinclude (6)option (1)post_thanks_box (1)post_thanks_button (1)post_thanks_javascript (1)post_thanks_navbar_search (1)post_thanks_postbit_info (1)postbit (1)postbit_onlinestatus (1)postbit_wrapper (1)spacer_close (1)spacer_open Phrase Groups Available: global postbit reputationlevel showthread	Included Files: ./showpost.php ./global.php ./includes/init.php ./includes/class_core.php ./includes/config.php ./includes/functions.php ./includes/class_hook.php ./includes/modsystem_functions.php ./includes/functions_bigthree.php ./includes/class_postbit.php ./includes/class_bbcode.php ./includes/functions_reputation.php ./includes/functions_post_thanks.php Hooks Called: init_startup init_startup_session_setup_start init_startup_session_setup_complete cache_permissions fetch_postinfo_query fetch_postinfo fetch_threadinfo_query fetch_threadinfo fetch_foruminfo style_fetch cache_templates global_start parse_templates global_setup_complete showpost_start bbcode_fetch_tags bbcode_create postbit_factory showpost_post postbit_display_start post_thanks_function_post_thanks_off_start post_thanks_function_post_thanks_off_end post_thanks_function_fetch_thanks_start post_thanks_function_fetch_thanks_end post_thanks_function_thanked_already_start post_thanks_function_thanked_already_end fetch_musername postbit_imicons bbcode_parse_start bbcode_parse_complete_precache bbcode_parse_complete postbit_display_complete post_thanks_function_can_thank_this_post_start showpost_complete
Messages: