diff --git a/doxygen.conf b/doxygen.conf
index d39e9ef64..4db530d40 100644
--- a/doxygen.conf
+++ b/doxygen.conf
@@ -51,7 +51,7 @@ PROJECT_BRIEF          =
 # and the maximum width should not exceed 200 pixels. Doxygen will copy the logo
 # to the output directory.
 
-PROJECT_LOGO           = "/home/jenkins/PocketMine-h-64.png"
+PROJECT_LOGO           =
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
 # into which the generated documentation will be written. If a relative path is
@@ -240,7 +240,7 @@ OPTIMIZE_OUTPUT_FOR_C  = NO
 # qualified scopes will look different, etc.
 # The default value is: NO.
 
-OPTIMIZE_OUTPUT_JAVA   = YES
+OPTIMIZE_OUTPUT_JAVA   = NO
 
 # Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
 # sources. Doxygen will then generate output that is tailored for Fortran.
@@ -737,7 +737,9 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ./
+INPUT                  = ./src \
+                         ./vendor/pocketmine \
+                         ./README.md
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -757,9 +759,7 @@ INPUT_ENCODING         = UTF-8
 # *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf,
 # *.qsf, *.as and *.js.
 
-FILE_PATTERNS          = *.php \
-                         *.sh \
-                         *.md
+FILE_PATTERNS          = *.php
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
 # be searched for input files as well.
@@ -793,7 +793,10 @@ EXCLUDE_SYMLINKS       = YES
 EXCLUDE_PATTERNS       = */bin/* \
                          */players/* \
                          */worlds/* \
-                         */plugins/*
+                         */plugins/* \
+                         */plugin_data/* \
+                         */tests/* \
+                         */stubs/*
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
@@ -878,7 +881,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE = README.md
+USE_MDFILE_AS_MAINPAGE = ./README.md
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing