diff --git a/config_gen.py b/config_gen.py
index 6089b20..c44bf1c 100755
--- a/config_gen.py
+++ b/config_gen.py
@@ -420,7 +420,7 @@ def parse_flags(build_log):
     # -warnings (-Werror), but no assembler, etc. flags (-Wa,-option)
     # -language (-std=gnu99) and standard library (-nostdlib)
     # -word size (-m64)
-    flags_whitelist = ["-[iIDF].*", "-W[^,]*", "-std=[a-z0-9+]+", "-(no)?std(lib|inc)", "-m[0-9]+"]
+    flags_whitelist = ["-[iIDF].*", "-W[^,]*", "-std=[a-z0-9+]+", "-(no)?std(lib|inc)", "-m[0-9]+", "-target"]
     flags_whitelist = re.compile("|".join(map("^{}$".format, flags_whitelist)))
     flags = set()
     line_count = 0
@@ -430,7 +430,7 @@ def parse_flags(build_log):
     define_regex = re.compile("-D([a-zA-Z0-9_]+)=(.*)")
 
     # Used to only bundle filenames with applicable arguments
-    filename_flags = ["-o", "-I", "-isystem", "-iquote", "-include", "-imacros", "-isysroot"]
+    filename_flags = ["-o", "-I", "-isystem", "-iquote", "-include", "-imacros", "-isysroot", "-target"]
 
     # Process build log
     for line in build_log:
diff --git a/fake-toolchain/Unix/arm-none-eabi-g++ b/fake-toolchain/Unix/arm-none-eabi-g++
deleted file mode 120000
index 34836c6..0000000
--- a/fake-toolchain/Unix/arm-none-eabi-g++
+++ /dev/null
@@ -1 +0,0 @@
-cxx
\ No newline at end of file
diff --git a/fake-toolchain/Unix/arm-none-eabi-g++ b/fake-toolchain/Unix/arm-none-eabi-g++
new file mode 100755
index 0000000..f3be24e
--- /dev/null
+++ b/fake-toolchain/Unix/arm-none-eabi-g++
@@ -0,0 +1,14 @@
+#!/bin/sh
+
+if [ ! -z "$YCM_CONFIG_GEN_CC_PASSTHROUGH" ]; then
+    # Cmake determines compiler properties by compiling a test file, so call clang for this case
+    $YCM_CONFIG_GEN_CXX_PASSTHROUGH $@
+
+elif [ "$1" = "-v" ] || [ "$1" = "--version" ]; then
+    # Needed to enable clang-specific options for certain build systems (e.g. linux)
+    $YCM_CONFIG_GEN_CXX_PASSTHROUGH $@
+
+else
+    echo "$@" >> $YCM_CONFIG_GEN_CXX_LOG -target arm-none-eabi
+fi
+
diff --git a/fake-toolchain/Unix/arm-none-eabi-gcc b/fake-toolchain/Unix/arm-none-eabi-gcc
deleted file mode 120000
index 2652f5f..0000000
--- a/fake-toolchain/Unix/arm-none-eabi-gcc
+++ /dev/null
@@ -1 +0,0 @@
-cc
\ No newline at end of file
diff --git a/fake-toolchain/Unix/arm-none-eabi-gcc b/fake-toolchain/Unix/arm-none-eabi-gcc
new file mode 100755
index 0000000..7749714
--- /dev/null
+++ b/fake-toolchain/Unix/arm-none-eabi-gcc
@@ -0,0 +1,14 @@
+#!/bin/sh
+
+if [ ! -z "$YCM_CONFIG_GEN_CC_PASSTHROUGH" ]; then
+    # Cmake determines compiler properties by compiling a test file, so call clang for this case
+    $YCM_CONFIG_GEN_CC_PASSTHROUGH $@
+
+elif [ "$1" = "-v" ] || [ "$1" = "--version" ]; then
+    # Needed to enable clang-specific options for certain build systems (e.g. linux)
+    $YCM_CONFIG_GEN_CC_PASSTHROUGH $@
+
+else
+    echo "$@" >> $YCM_CONFIG_GEN_CC_LOG -target arm-none-eabi
+fi
+
diff --git a/fake-toolchain/Unix/avr-g++ b/fake-toolchain/Unix/avr-g++
deleted file mode 120000
index 34836c6..0000000
--- a/fake-toolchain/Unix/avr-g++
+++ /dev/null
@@ -1 +0,0 @@
-cxx
\ No newline at end of file
diff --git a/fake-toolchain/Unix/avr-g++ b/fake-toolchain/Unix/avr-g++
new file mode 100755
index 0000000..03b56b9
--- /dev/null
+++ b/fake-toolchain/Unix/avr-g++
@@ -0,0 +1,16 @@
+#!/bin/sh
+
+AVR_LIB=$(cat /tmp/avr_gcc_include)
+
+if [ ! -z "$YCM_CONFIG_GEN_CC_PASSTHROUGH" ]; then
+    # Cmake determines compiler properties by compiling a test file, so call clang for this case
+    $YCM_CONFIG_GEN_CXX_PASSTHROUGH $@
+
+elif [ "$1" = "-v" ] || [ "$1" = "--version" ]; then
+    # Needed to enable clang-specific options for certain build systems (e.g. linux)
+    $YCM_CONFIG_GEN_CXX_PASSTHROUGH $@
+
+else
+    echo "$@" >> $YCM_CONFIG_GEN_CXX_LOG -isystem $AVR_LIB -D__flash= --target=avr
+fi
+
diff --git a/fake-toolchain/Unix/avr-gcc b/fake-toolchain/Unix/avr-gcc
deleted file mode 120000
index 2652f5f..0000000
--- a/fake-toolchain/Unix/avr-gcc
+++ /dev/null
@@ -1 +0,0 @@
-cc
\ No newline at end of file
diff --git a/fake-toolchain/Unix/avr-gcc b/fake-toolchain/Unix/avr-gcc
new file mode 100755
index 0000000..ce7b1cf
--- /dev/null
+++ b/fake-toolchain/Unix/avr-gcc
@@ -0,0 +1,16 @@
+#!/bin/sh
+
+AVR_LIB=$(cat /tmp/avr_gcc_include)
+
+if [ ! -z "$YCM_CONFIG_GEN_CC_PASSTHROUGH" ]; then
+    # Cmake determines compiler properties by compiling a test file, so call clang for this case
+    $YCM_CONFIG_GEN_CC_PASSTHROUGH $@
+
+elif [ "$1" = "-v" ] || [ "$1" = "--version" ]; then
+    # Needed to enable clang-specific options for certain build systems (e.g. linux)
+    $YCM_CONFIG_GEN_CC_PASSTHROUGH $@
+
+else
+    echo "$@" >> $YCM_CONFIG_GEN_CC_LOG -isystem $AVR_LIB -D__flash= --target=avr
+fi
+
diff --git a/template.py b/template.py
index 7f52bb4..8c33760 100644
--- a/template.py
+++ b/template.py
@@ -36,11 +36,22 @@
 import re
 import subprocess
 
+import os.path as p
+import sys
+
+DIR_OF_THIS = p.abspath(p.dirname(__file__))
+sys.path.append(DIR_OF_THIS)
+
+try:
+    from ycm_extra_manual_config import extra_flags
+except ImportError:
+    extra_flags = []
 
 flags = [
     # INSERT FLAGS HERE
 ]
 
+flags += extra_flags
 
 def LoadSystemIncludes():
     regex = re.compile(r'(?:\#include \<...\> search starts here\:)(?P<list>.*?)(?:End of search list)', re.DOTALL)