diff --git a/docs b/docs
index 437b1175..890d8e20 160000
--- a/docs
+++ b/docs
@@ -1 +1 @@
-Subproject commit 437b1175bdb310e143f1fe6312433ba4f34ef715
+Subproject commit 890d8e20fed40f653ac84ff366ac16d805b4bf01
diff --git a/platformio/builder/tools/piobuild.py b/platformio/builder/tools/piobuild.py
index ba194eb0..79e2c39b 100644
--- a/platformio/builder/tools/piobuild.py
+++ b/platformio/builder/tools/piobuild.py
@@ -200,7 +200,7 @@ def ParseFlagsExtended(env, flags):  # pylint: disable=too-many-branches
     # fix relative CPPPATH & LIBPATH
     for k in ("CPPPATH", "LIBPATH"):
         for i, p in enumerate(result.get(k, [])):
-            if os.path.isdir(p):
+            if not os.path.isabs(p):
                 result[k][i] = os.path.abspath(p)
 
     # fix relative path for "-include"
diff --git a/platformio/project/integration/generator.py b/platformio/project/integration/generator.py
index 12f53ef0..40b8e87a 100644
--- a/platformio/project/integration/generator.py
+++ b/platformio/project/integration/generator.py
@@ -134,7 +134,7 @@ class ProjectGenerator:
             for root, _, files in os.walk(self.config.get("platformio", "src_dir")):
                 for f in files:
                     result.append(
-                        os.path.relpath(os.path.join(os.path.realpath(root), f))
+                        os.path.relpath(os.path.join(os.path.abspath(root), f))
                     )
         return result
 
diff --git a/tests/commands/test_run.py b/tests/commands/test_run.py
index 009f33c9..cb9e3d85 100644
--- a/tests/commands/test_run.py
+++ b/tests/commands/test_run.py
@@ -22,6 +22,7 @@ def test_generic_build(clirunner, validate_cliresult, tmpdir):
         ("-D TEST_INT=13", "-DTEST_INT=13"),
         ("-DTEST_SINGLE_MACRO", "-DTEST_SINGLE_MACRO"),
         ('-DTEST_STR_SPACE="Andrew Smith"', '"-DTEST_STR_SPACE=Andrew Smith"'),
+        ("-Iextra_inc", "-Iextra_inc"),
     ]
 
     tmpdir.join("platformio.ini").write(
@@ -58,8 +59,20 @@ projenv.Append(CPPDEFINES="POST_SCRIPT_MACRO")
     """
     )
 
+    tmpdir.mkdir("extra_inc").join("foo.h").write(
+        """
+#define FOO
+    """
+    )
+
     tmpdir.mkdir("src").join("main.cpp").write(
         """
+#include "foo.h"
+
+#ifndef FOO
+#error "FOO"
+#endif
+
 #ifdef I_AM_ONLY_SRC_FLAG
 #include <component.h>
 #else