diff --git a/mesonbuild/backend/backends.py b/mesonbuild/backend/backends.py
index eadc8cce4..a83d95f27 100644
--- a/mesonbuild/backend/backends.py
+++ b/mesonbuild/backend/backends.py
@@ -21,6 +21,7 @@ from .. import compilers
 import json
 import subprocess
 from ..mesonlib import MesonException, get_compiler_for_source, classify_unity_sources
+from ..compilers import CompilerArgs
 
 class CleanTrees:
     '''
@@ -338,32 +339,59 @@ class Backend:
         return extra_args
 
     def generate_basic_compiler_args(self, target, compiler, no_warn_args=False):
-        commands = []
+        # Create an empty commands list, and start adding arguments from
+        # various sources in the order in which they must override each other
+        # starting from hard-coded defaults followed by build options and so on.
+        commands = CompilerArgs(compiler)
+        # First, the trivial ones that are impossible to override.
+        #
+        # Add -nostdinc/-nostdinc++ if needed; can't be overriden
         commands += self.get_cross_stdlib_args(target, compiler)
+        # Add things like /NOLOGO or -pipe; usually can't be overriden
         commands += compiler.get_always_args()
+        # Only add warning-flags by default if the buildtype enables it, and if
+        # we weren't explicitly asked to not emit warnings (for Vala, f.ex)
         if no_warn_args:
             commands += compiler.get_no_warn_args()
         elif self.environment.coredata.get_builtin_option('buildtype') != 'plain':
             commands += compiler.get_warn_args(self.environment.coredata.get_builtin_option('warning_level'))
+        # Add -Werror if werror=true is set in the build options set on the
+        # command-line or default_options inside project(). This only sets the
+        # action to be done for warnings if/when they are emitted, so it's ok
+        # to set it after get_no_warn_args() or get_warn_args().
+        if self.environment.coredata.get_builtin_option('werror'):
+            commands += compiler.get_werror_args()
+        # Add compile args for c_* or cpp_* build options set on the
+        # command-line or default_options inside project().
         commands += compiler.get_option_compile_args(self.environment.coredata.compiler_options)
-        commands += self.build.get_global_args(compiler)
+        # Add buildtype args: optimization level, debugging, etc.
+        commands += compiler.get_buildtype_args(self.environment.coredata.get_builtin_option('buildtype'))
+        # Add compile args added using add_project_arguments()
         commands += self.build.get_project_args(compiler, target.subproject)
+        # Add compile args added using add_global_arguments()
+        # These override per-project arguments
+        commands += self.build.get_global_args(compiler)
+        # Compile args added from the env: CFLAGS/CXXFLAGS, etc. We want these
+        # to override all the defaults, but not the per-target compile args.
         commands += self.environment.coredata.external_args[compiler.get_language()]
-        commands += self.escape_extra_args(compiler, target.get_extra_args(compiler.get_language()))
-        commands += compiler.get_buildtype_args(self.environment.coredata.get_builtin_option('buildtype'))
-        if self.environment.coredata.get_builtin_option('werror'):
-            commands += compiler.get_werror_args()
+        # Always set -fPIC for shared libraries
         if isinstance(target, build.SharedLibrary):
             commands += compiler.get_pic_args()
+        # Set -fPIC for static libraries by default unless explicitly disabled
         if isinstance(target, build.StaticLibrary) and target.pic:
             commands += compiler.get_pic_args()
+        # Add compile args needed to find external dependencies
+        # Link args are added while generating the link command
         for dep in target.get_external_deps():
-            # Cflags required by external deps might have UNIX-specific flags,
-            # so filter them out if needed
-            commands += compiler.unix_args_to_native(dep.get_compile_args())
+            commands += dep.get_compile_args()
+            # Qt needs -fPIC for executables
+            # XXX: We should move to -fPIC for all executables
             if isinstance(target, build.Executable):
-                commands += dep.get_exe_args()
-
+                commands += dep.get_exe_args(compiler)
+            # For 'automagic' deps: Boost and GTest. Also dependency('threads').
+            # pkg-config puts the thread flags itself via `Cflags:`
+            if dep.need_threads():
+                commands += compiler.thread_flags()
         # Fortran requires extra include directives.
         if compiler.language == 'fortran':
             for lt in target.link_targets:
diff --git a/mesonbuild/backend/ninjabackend.py b/mesonbuild/backend/ninjabackend.py
index 5bd660c3a..98740a4d0 100644
--- a/mesonbuild/backend/ninjabackend.py
+++ b/mesonbuild/backend/ninjabackend.py
@@ -19,6 +19,7 @@ from .. import build
 from .. import mlog
 from .. import dependencies
 from .. import compilers
+from ..compilers import CompilerArgs
 from ..mesonlib import File, MesonException, get_compiler_for_source, Popen_safe
 from .backends import CleanTrees, InstallData
 from ..build import InvalidArguments
@@ -1725,7 +1726,7 @@ rule FORTRAN_DEP_HACK
 
     def generate_llvm_ir_compile(self, target, outfile, src):
         compiler = get_compiler_for_source(target.compilers.values(), src)
-        commands = []
+        commands = CompilerArgs(compiler)
         # Compiler args for compiling this target
         commands += compilers.get_base_compile_args(self.environment.coredata.base_options,
                                                     compiler)
@@ -1748,11 +1749,40 @@ rule FORTRAN_DEP_HACK
         # Write the Ninja build command
         compiler_name = 'llvm_ir{}_COMPILER'.format('_CROSS' if target.is_cross else '')
         element = NinjaBuildElement(self.all_outputs, rel_obj, compiler_name, rel_src)
-        commands = self.dedup_arguments(commands)
+        # Convert from GCC-style link argument naming to the naming used by the
+        # current compiler.
+        commands = commands.to_native()
         element.add_item('ARGS', commands)
         element.write(outfile)
         return rel_obj
 
+    def get_source_dir_include_args(self, target, compiler):
+        curdir = target.get_subdir()
+        tmppath = os.path.normpath(os.path.join(self.build_to_src, curdir))
+        return compiler.get_include_args(tmppath, False)
+
+    def get_build_dir_include_args(self, target, compiler):
+        curdir = target.get_subdir()
+        if curdir == '':
+            curdir = '.'
+        return compiler.get_include_args(curdir, False)
+
+    def get_custom_target_dir_include_args(self, target, compiler):
+        custom_target_include_dirs = []
+        for i in target.get_generated_sources():
+            # Generator output goes into the target private dir which is
+            # already in the include paths list. Only custom targets have their
+            # own target build dir.
+            if not isinstance(i, build.CustomTarget):
+                continue
+            idir = self.get_target_dir(i)
+            if idir not in custom_target_include_dirs:
+                custom_target_include_dirs.append(idir)
+        incs = []
+        for i in custom_target_include_dirs:
+            incs += compiler.get_include_args(i, False)
+        return incs
+
     def generate_single_compile(self, target, outfile, src, is_generated=False, header_deps=[], order_deps=[]):
         """
         Compiles C/C++, ObjC/ObjC++, Fortran, and D sources
@@ -1763,30 +1793,40 @@ rule FORTRAN_DEP_HACK
             raise AssertionError('BUG: sources should not contain headers {!r}'.format(src.fname))
         extra_orderdeps = []
         compiler = get_compiler_for_source(target.compilers.values(), src)
-        commands = []
-        # The first thing is implicit include directories: source, build and private.
-        commands += compiler.get_include_args(self.get_target_private_dir(target), False)
-        # Compiler args for compiling this target
+
+        # Create an empty commands list, and start adding arguments from
+        # various sources in the order in which they must override each other
+        commands = CompilerArgs(compiler)
+        # Add compiler args for compiling this target derived from 'base' build
+        # options passed on the command-line, in default_options, etc.
+        # These have the lowest priority.
         commands += compilers.get_base_compile_args(self.environment.coredata.base_options,
                                                     compiler)
-        # Add the root source and build directories as include dirs
-        curdir = target.get_subdir()
-        tmppath = os.path.normpath(os.path.join(self.build_to_src, curdir))
-        src_inc = compiler.get_include_args(tmppath, False)
-        if curdir == '':
-            curdir = '.'
-        build_inc = compiler.get_include_args(curdir, False)
-        commands += build_inc + src_inc
-        # -I args work differently than other ones. In them the first found
-        # directory is used whereas for other flags (such as -ffoo -fno-foo) the
-        # latest one is used.  Therefore put the internal include directories
-        # here before generating the "basic compiler args" so they override args
-        # coming from e.g. pkg-config.
+        # The code generated by valac is usually crap and has tons of unused
+        # variables and such, so disable warnings for Vala C sources.
+        no_warn_args = (is_generated == 'vala')
+        # Add compiler args and include paths from several sources; defaults,
+        # build options, external dependencies, etc.
+        commands += self.generate_basic_compiler_args(target, compiler, no_warn_args)
+        # Add include dirs from the `include_directories:` kwarg on the target
+        # and from `include_directories:` of internal deps of the target.
+        #
+        # Target include dirs should override internal deps include dirs.
+        #
+        # Include dirs from internal deps should override include dirs from
+        # external deps.
         for i in target.get_include_dirs():
             basedir = i.get_curdir()
             for d in i.get_incdirs():
-                expdir = os.path.join(basedir, d)
+                # Avoid superfluous '/.' at the end of paths when d is '.'
+                if d not in ('', '.'):
+                    expdir = os.path.join(basedir, d)
+                else:
+                    expdir = basedir
                 srctreedir = os.path.join(self.build_to_src, expdir)
+                # Add source subdir first so that the build subdir overrides it
+                sargs = compiler.get_include_args(srctreedir, i.is_system)
+                commands += sargs
                 # There may be include dirs where a build directory has not been
                 # created for some source dir. For example if someone does this:
                 #
@@ -1797,20 +1837,32 @@ rule FORTRAN_DEP_HACK
                     bargs = compiler.get_include_args(expdir, i.is_system)
                 else:
                     bargs = []
-                sargs = compiler.get_include_args(srctreedir, i.is_system)
                 commands += bargs
-                commands += sargs
             for d in i.get_extra_build_dirs():
                 commands += compiler.get_include_args(d, i.is_system)
-        commands += self.generate_basic_compiler_args(target, compiler,
-                                                      # The code generated by valac is usually crap
-                                                      # and has tons of unused variables and such,
-                                                      # so disable warnings for Vala C sources.
-                                                      no_warn_args=(is_generated == 'vala'))
-        for d in target.external_deps:
-            if d.need_threads():
-                commands += compiler.thread_flags()
-                break
+        # Add per-target compile args, f.ex, `c_args : ['-DFOO']`. We set these
+        # near the end since these are supposed to override everything else.
+        commands += self.escape_extra_args(compiler,
+                                           target.get_extra_args(compiler.get_language()))
+        # Add source dir and build dir. Project-specific and target-specific
+        # include paths must override per-target compile args, include paths
+        # from external dependencies, internal dependencies, and from
+        # per-target `include_directories:`
+        #
+        # We prefer headers in the build dir and the custom target dir over the
+        # source dir since, for instance, the user might have an
+        # srcdir == builddir Autotools build in their source tree. Many
+        # projects that are moving to Meson have both Meson and Autotools in
+        # parallel as part of the transition.
+        commands += self.get_source_dir_include_args(target, compiler)
+        commands += self.get_custom_target_dir_include_args(target, compiler)
+        commands += self.get_build_dir_include_args(target, compiler)
+        # Finally add the private dir for the target to the include path. This
+        # must override everything else and must be the final path added.
+        commands += compiler.get_include_args(self.get_target_private_dir(target), False)
+
+        # FIXME: This file handling is atrocious and broken. We need to
+        # replace it with File objects used consistently everywhere.
         if isinstance(src, RawFilename):
             rel_src = src.fname
             if os.path.isabs(src.fname):
@@ -1835,7 +1887,13 @@ rule FORTRAN_DEP_HACK
         rel_obj = os.path.join(self.get_target_private_dir(target), obj_basename)
         rel_obj += '.' + self.environment.get_object_suffix()
         dep_file = compiler.depfile_for_object(rel_obj)
+
+        # Add MSVC debug file generation compile flags: /Fd /FS
+        commands += self.get_compile_debugfile_args(compiler, target, rel_obj)
+
+        # PCH handling
         if self.environment.coredata.base_options.get('b_pch', False):
+            commands += self.get_pch_include_args(compiler, target)
             pchlist = target.get_pch(compiler.language)
         else:
             pchlist = []
@@ -1848,19 +1906,7 @@ rule FORTRAN_DEP_HACK
             i = os.path.join(self.get_target_private_dir(target), compiler.get_pch_name(pchlist[0]))
             arr.append(i)
             pch_dep = arr
-        custom_target_include_dirs = []
-        for i in target.get_generated_sources():
-            if not isinstance(i, build.CustomTarget):
-                continue
-            idir = self.get_target_dir(i)
-            if idir not in custom_target_include_dirs:
-                custom_target_include_dirs.append(idir)
-        for i in custom_target_include_dirs:
-            commands += compiler.get_include_args(i, False)
-        if self.environment.coredata.base_options.get('b_pch', False):
-            commands += self.get_pch_include_args(compiler, target)
 
-        commands += self.get_compile_debugfile_args(compiler, target, rel_obj)
         crstr = ''
         if target.is_cross:
             crstr = '_CROSS'
@@ -1895,7 +1941,9 @@ rule FORTRAN_DEP_HACK
             element.add_orderdep(d)
         element.add_orderdep(pch_dep)
         element.add_orderdep(extra_orderdeps)
-        commands = self.dedup_arguments(commands)
+        # Convert from GCC-style link argument naming to the naming used by the
+        # current compiler.
+        commands = commands.to_native()
         for i in self.get_fortran_orderdeps(target, compiler):
             element.add_orderdep(i)
         element.add_item('DEPFILE', dep_file)
diff --git a/mesonbuild/build.py b/mesonbuild/build.py
index a9f08c3ee..e5d228484 100644
--- a/mesonbuild/build.py
+++ b/mesonbuild/build.py
@@ -585,14 +585,16 @@ class BuildTarget(Target):
         for i in self.link_depends:
             if not isinstance(i, str):
                 raise InvalidArguments('Link_depends arguments must be strings.')
-        inclist = kwargs.get('include_directories', [])
-        if not isinstance(inclist, list):
-            inclist = [inclist]
-        self.add_include_dirs(inclist)
         deplist = kwargs.get('dependencies', [])
         if not isinstance(deplist, list):
             deplist = [deplist]
         self.add_deps(deplist)
+        # Target-specific include dirs must be added after include dirs from
+        # internal deps (added inside self.add_deps()) to override correctly.
+        inclist = kwargs.get('include_directories', [])
+        if not isinstance(inclist, list):
+            inclist = [inclist]
+        self.add_include_dirs(inclist)
         self.custom_install_dir = kwargs.get('install_dir', None)
         if self.custom_install_dir is not None:
             if not isinstance(self.custom_install_dir, str):
diff --git a/mesonbuild/coredata.py b/mesonbuild/coredata.py
index 60bb10bc5..1ec769a36 100644
--- a/mesonbuild/coredata.py
+++ b/mesonbuild/coredata.py
@@ -117,7 +117,9 @@ class CoreData:
         self.user_options = {}
         self.compiler_options = {}
         self.base_options = {}
-        self.external_args = {} # These are set from "the outside" with e.g. mesonconf
+        # These two, external_*args, are set via env vars CFLAGS, LDFLAGS, etc
+        # but only when not cross-compiling.
+        self.external_args = {}
         self.external_link_args = {}
         if options.cross_file is not None:
             self.cross_file = os.path.join(os.getcwd(), options.cross_file)
diff --git a/mesonbuild/dependencies.py b/mesonbuild/dependencies.py
index 6ae91d456..b01e0a899 100644
--- a/mesonbuild/dependencies.py
+++ b/mesonbuild/dependencies.py
@@ -59,7 +59,7 @@ class Dependency:
     def get_name(self):
         return self.name
 
-    def get_exe_args(self):
+    def get_exe_args(self, compiler):
         return []
 
     def need_threads(self):
@@ -1045,16 +1045,14 @@ class QtBaseDependency(Dependency):
     def found(self):
         return self.is_found
 
-    def get_exe_args(self):
+    def get_exe_args(self, compiler):
         # Originally this was -fPIE but nowadays the default
         # for upstream and distros seems to be -reduce-relocations
         # which requires -fPIC. This may cause a performance
         # penalty when using self-built Qt or on platforms
         # where -fPIC is not required. If this is an issue
         # for you, patches are welcome.
-        if mesonlib.is_linux():
-            return ['-fPIC']
-        return []
+        return compiler.get_pic_args()
 
 class Qt5Dependency(QtBaseDependency):
     def __init__(self, env, kwargs):
diff --git a/run_unittests.py b/run_unittests.py
index a90e46b5d..b6ea073c4 100755
--- a/run_unittests.py
+++ b/run_unittests.py
@@ -14,6 +14,7 @@
 # limitations under the License.
 
 import stat
+import shlex
 import unittest, os, sys, shutil, time
 import subprocess
 import re, json
@@ -698,6 +699,38 @@ class LinuxlikeTests(unittest.TestCase):
             # The chown failed nonfatally if we're not root
             self.assertEqual(0, statf.st_uid)
 
+    def test_internal_include_order(self):
+        testdir = os.path.join(self.common_test_dir, '138 include order')
+        self.init(testdir)
+        for cmd in self.get_compdb():
+            if cmd['file'].endswith('/main.c'):
+                cmd = cmd['command']
+                break
+        else:
+            raise Exception('Could not find main.c command')
+        incs = [a for a in shlex.split(cmd) if a.startswith("-I")]
+        self.assertEqual(len(incs), 8)
+        # target private dir
+        self.assertEqual(incs[0], "-Isub4/someexe@exe")
+        # target build subdir
+        self.assertEqual(incs[1], "-Isub4")
+        # target source subdir
+        msg = "{!r} does not end with '/sub4'".format(incs[2])
+        self.assertTrue(incs[2].endswith("/sub4"), msg)
+        # include paths added via per-target c_args: ['-I'...]
+        msg = "{!r} does not end with '/sub3'".format(incs[3])
+        self.assertTrue(incs[3].endswith("/sub3"), msg)
+        # target include_directories: build dir
+        self.assertEqual(incs[4], "-Isub2")
+        # target include_directories: source dir
+        msg = "{!r} does not end with '/sub2'".format(incs[5])
+        self.assertTrue(incs[5].endswith("/sub2"), msg)
+        # target internal dependency include_directories: build dir
+        self.assertEqual(incs[6], "-Isub1")
+        # target internal dependency include_directories: source dir
+        msg = "{!r} does not end with '/sub1'".format(incs[7])
+        self.assertTrue(incs[7].endswith("/sub1"), msg)
+
 
 class RewriterTests(unittest.TestCase):
 
diff --git a/test cases/common/138 include order/meson.build b/test cases/common/138 include order/meson.build
new file mode 100644
index 000000000..f744ae766
--- /dev/null
+++ b/test cases/common/138 include order/meson.build	
@@ -0,0 +1,22 @@
+project('include order', 'c')
+
+# Test that the order of priority of include paths (from first to last) is:
+#
+# 1. Target's current build directory
+# 2. Target's current source directory
+# 3. Include paths added with the `c_args:` kwarg
+# 4. Include paths added with the `include_directories`: kwarg
+#    Within this, the build dir takes precedence over the source dir
+# 5. Include paths added via `include_directories:` of internal deps
+#    Within this, the build dir takes precedence over the source dir
+
+# Defines an internal dep
+subdir('sub1')
+# Defines a per-target include path
+subdir('sub2')
+# Directory for `c_args:` include path
+subdir('sub3')
+# The directory where the target resides
+subdir('sub4')
+
+test('eh', e)
diff --git a/test cases/common/138 include order/sub1/main.h b/test cases/common/138 include order/sub1/main.h
new file mode 100644
index 000000000..acf4a358c
--- /dev/null
+++ b/test cases/common/138 include order/sub1/main.h	
@@ -0,0 +1 @@
+#error "sub1/main.h included"
diff --git a/test cases/common/138 include order/sub1/meson.build b/test cases/common/138 include order/sub1/meson.build
new file mode 100644
index 000000000..9672945b6
--- /dev/null
+++ b/test cases/common/138 include order/sub1/meson.build	
@@ -0,0 +1,4 @@
+i = include_directories('.')
+l = shared_library('somelib', 'some.c')
+dep = declare_dependency(link_with : l,
+                         include_directories : i)
diff --git a/test cases/common/138 include order/sub1/some.c b/test cases/common/138 include order/sub1/some.c
new file mode 100644
index 000000000..1ab0db4dd
--- /dev/null
+++ b/test cases/common/138 include order/sub1/some.c	
@@ -0,0 +1,6 @@
+#if defined _WIN32 || defined __CYGWIN__
+  __declspec(dllexport)
+#endif
+int somefunc(void) {
+  return 1984;
+}
diff --git a/test cases/common/138 include order/sub1/some.h b/test cases/common/138 include order/sub1/some.h
new file mode 100644
index 000000000..6479492ea
--- /dev/null
+++ b/test cases/common/138 include order/sub1/some.h	
@@ -0,0 +1,10 @@
+#pragma once
+
+#if defined _WIN32 || defined __CYGWIN__
+  #define DLL_PUBLIC __declspec(dllimport)
+#else
+  #define DLL_PUBLIC
+#endif
+
+DLL_PUBLIC
+int somefunc(void);
diff --git a/test cases/common/138 include order/sub2/main.h b/test cases/common/138 include order/sub2/main.h
new file mode 100644
index 000000000..b9c0da93a
--- /dev/null
+++ b/test cases/common/138 include order/sub2/main.h	
@@ -0,0 +1 @@
+#error "sub2/main.h included"
diff --git a/test cases/common/138 include order/sub2/meson.build b/test cases/common/138 include order/sub2/meson.build
new file mode 100644
index 000000000..7b49d6af1
--- /dev/null
+++ b/test cases/common/138 include order/sub2/meson.build	
@@ -0,0 +1 @@
+j = include_directories('.')
diff --git a/test cases/common/138 include order/sub3/main.h b/test cases/common/138 include order/sub3/main.h
new file mode 100644
index 000000000..1ab723141
--- /dev/null
+++ b/test cases/common/138 include order/sub3/main.h	
@@ -0,0 +1 @@
+#error "sub3/main.h included"
diff --git a/test cases/common/138 include order/sub3/meson.build b/test cases/common/138 include order/sub3/meson.build
new file mode 100644
index 000000000..0bd3906c1
--- /dev/null
+++ b/test cases/common/138 include order/sub3/meson.build	
@@ -0,0 +1 @@
+sub3 = meson.current_source_dir()
diff --git a/test cases/common/138 include order/sub4/main.c b/test cases/common/138 include order/sub4/main.c
new file mode 100644
index 000000000..0b25eedfe
--- /dev/null
+++ b/test cases/common/138 include order/sub4/main.c	
@@ -0,0 +1,8 @@
+/* Use the <> include notation to force searching in include directories */
+#include <main.h>
+
+int main(int argc, char *argv[]) {
+  if (somefunc() == 1984)
+    return 0;
+  return 1;
+}
diff --git a/test cases/common/138 include order/sub4/main.h b/test cases/common/138 include order/sub4/main.h
new file mode 100644
index 000000000..194d7fe5f
--- /dev/null
+++ b/test cases/common/138 include order/sub4/main.h	
@@ -0,0 +1,3 @@
+#pragma once
+
+#include "some.h"
diff --git a/test cases/common/138 include order/sub4/meson.build b/test cases/common/138 include order/sub4/meson.build
new file mode 100644
index 000000000..538899aaa
--- /dev/null
+++ b/test cases/common/138 include order/sub4/meson.build	
@@ -0,0 +1,4 @@
+e = executable('someexe', 'main.c',
+               c_args : ['-I' + sub3],
+               include_directories : j,
+               dependencies : dep)