diff --git a/source/dub/packagemanager.d b/source/dub/packagemanager.d
index 0777f19..f31f597 100644
--- a/source/dub/packagemanager.d
+++ b/source/dub/packagemanager.d
@@ -1438,30 +1438,41 @@
 			logDebug("iterating dir %s entry %s", path.toNativeString(), pdir.name);
 			if (!pdir.isDirectory) continue;
 
-			// Old / flat directory structure, used in non-standard path
-			// Packages are stored in $ROOT/$SOMETHING/`
 			const pack_path = path ~ (pdir.name ~ "/");
 			auto packageFile = Package.findPackageFile(pack_path);
-			if (!packageFile.empty) {
-				// Deprecated unmanaged directory structure
-				logWarn("Package at path '%s' should be under '%s'",
-						pack_path.toNativeString().color(Mode.bold),
-						(pack_path ~ "$VERSION" ~ pdir.name).toNativeString().color(Mode.bold));
-				logWarn("The package will no longer be detected starting from v1.42.0");
-				loadInternal(pack_path, packageFile);
-			}
 
-			// Managed structure: $ROOT/$NAME/$VERSION/$NAME
-			// This is the most common code path
-			else {
-				// Iterate over versions of a package
-				foreach (versdir; mgr.iterateDirectory(pack_path)) {
-					if (!versdir.isDirectory) continue;
-					auto vers_path = pack_path ~ versdir.name ~ (pdir.name ~ "/");
-					if (!mgr.existsDirectory(vers_path)) continue;
-					packageFile = Package.findPackageFile(vers_path);
-					loadInternal(vers_path, packageFile);
+			if (isManaged(path)) {
+				// Old / flat directory structure, used in non-standard path
+				// Packages are stored in $ROOT/$SOMETHING/`
+				if (!packageFile.empty) {
+					// Deprecated flat managed directory structure
+					logWarn("Package at path '%s' should be under '%s'",
+							pack_path.toNativeString().color(Mode.bold),
+							(pack_path ~ "$VERSION" ~ pdir.name).toNativeString().color(Mode.bold));
+					logWarn("The package will no longer be detected starting from v1.42.0");
+					loadInternal(pack_path, packageFile);
+				} else {
+					// New managed structure: $ROOT/$NAME/$VERSION/$NAME
+					// This is the most common code path
+
+					// Iterate over versions of a package
+					foreach (versdir; mgr.iterateDirectory(pack_path)) {
+						if (!versdir.isDirectory) continue;
+						auto vers_path = pack_path ~ versdir.name ~ (pdir.name ~ "/");
+						if (!mgr.existsDirectory(vers_path)) continue;
+						packageFile = Package.findPackageFile(vers_path);
+						loadInternal(vers_path, packageFile);
+					}
 				}
+			} else {
+				// Unmanaged directories (dub add-path) are always stored as a
+				// flat list of packages, as these are the working copies managed
+				// by the user. The nested structure should not be supported,
+				// even optionally, because that would lead to bogus "no package
+				// file found" errors in case the internal directory structure
+				// accidentally matches the $NAME/$VERSION/$NAME scheme
+				if (!packageFile.empty)
+					loadInternal(pack_path, packageFile);
 			}
 		}
 		catch (Exception e)
diff --git a/test/issue1005-configuration-resolution/a/1.0.0/a/dub.sdl b/test/issue1005-configuration-resolution/a/1.0.0/a/dub.sdl
deleted file mode 100644
index d19952b..0000000
--- a/test/issue1005-configuration-resolution/a/1.0.0/a/dub.sdl
+++ /dev/null
@@ -1,10 +0,0 @@
-name "a"
-dependency "b" version="*"
-
-configuration "x" {
-	subConfiguration "b" "x"
-}
-
-configuration "y" {
-	subConfiguration "b" "y"
-}
diff --git a/test/issue1005-configuration-resolution/a/dub.sdl b/test/issue1005-configuration-resolution/a/dub.sdl
new file mode 100644
index 0000000..d19952b
--- /dev/null
+++ b/test/issue1005-configuration-resolution/a/dub.sdl
@@ -0,0 +1,10 @@
+name "a"
+dependency "b" version="*"
+
+configuration "x" {
+	subConfiguration "b" "x"
+}
+
+configuration "y" {
+	subConfiguration "b" "y"
+}
diff --git a/test/issue1005-configuration-resolution/b/1.0.0/b/dub.sdl b/test/issue1005-configuration-resolution/b/1.0.0/b/dub.sdl
deleted file mode 100644
index 3cfa48b..0000000
--- a/test/issue1005-configuration-resolution/b/1.0.0/b/dub.sdl
+++ /dev/null
@@ -1,7 +0,0 @@
-name "b"
-
-configuration "x" {
-}
-
-configuration "y" {
-}
\ No newline at end of file
diff --git a/test/issue1005-configuration-resolution/b/1.0.0/b/source/b.d b/test/issue1005-configuration-resolution/b/1.0.0/b/source/b.d
deleted file mode 100644
index 2a9bb41..0000000
--- a/test/issue1005-configuration-resolution/b/1.0.0/b/source/b.d
+++ /dev/null
@@ -1,3 +0,0 @@
-module b;
-
-void foo() {}
diff --git a/test/issue1005-configuration-resolution/b/dub.sdl b/test/issue1005-configuration-resolution/b/dub.sdl
new file mode 100644
index 0000000..3cfa48b
--- /dev/null
+++ b/test/issue1005-configuration-resolution/b/dub.sdl
@@ -0,0 +1,7 @@
+name "b"
+
+configuration "x" {
+}
+
+configuration "y" {
+}
\ No newline at end of file
diff --git a/test/issue1005-configuration-resolution/b/source/b.d b/test/issue1005-configuration-resolution/b/source/b.d
new file mode 100644
index 0000000..2a9bb41
--- /dev/null
+++ b/test/issue1005-configuration-resolution/b/source/b.d
@@ -0,0 +1,3 @@
+module b;
+
+void foo() {}
diff --git a/test/issue1005-configuration-resolution/c/1.0.0/c/dub.sdl b/test/issue1005-configuration-resolution/c/1.0.0/c/dub.sdl
deleted file mode 100644
index e46b148..0000000
--- a/test/issue1005-configuration-resolution/c/1.0.0/c/dub.sdl
+++ /dev/null
@@ -1,2 +0,0 @@
-name "c"
-dependency "a" version="*"
diff --git a/test/issue1005-configuration-resolution/c/dub.sdl b/test/issue1005-configuration-resolution/c/dub.sdl
new file mode 100644
index 0000000..e46b148
--- /dev/null
+++ b/test/issue1005-configuration-resolution/c/dub.sdl
@@ -0,0 +1,2 @@
+name "c"
+dependency "a" version="*"
diff --git a/test/issue1005-configuration-resolution/main/dub.sdl b/test/issue1005-configuration-resolution/main/dub.sdl
new file mode 100644
index 0000000..d492491
--- /dev/null
+++ b/test/issue1005-configuration-resolution/main/dub.sdl
@@ -0,0 +1,6 @@
+name "main"
+
+dependency "b" version="*"
+dependency "c" version="*"
+
+subConfiguration "b" "y"
diff --git a/test/issue1005-configuration-resolution/main/source/app.d b/test/issue1005-configuration-resolution/main/source/app.d
new file mode 100644
index 0000000..0ec7361
--- /dev/null
+++ b/test/issue1005-configuration-resolution/main/source/app.d
@@ -0,0 +1,6 @@
+import b;
+
+void main()
+{
+	foo();
+}
diff --git a/test/issue1005-configuration-resolution/main/~master/main/dub.sdl b/test/issue1005-configuration-resolution/main/~master/main/dub.sdl
deleted file mode 100644
index d492491..0000000
--- a/test/issue1005-configuration-resolution/main/~master/main/dub.sdl
+++ /dev/null
@@ -1,6 +0,0 @@
-name "main"
-
-dependency "b" version="*"
-dependency "c" version="*"
-
-subConfiguration "b" "y"
diff --git a/test/issue1005-configuration-resolution/main/~master/main/source/app.d b/test/issue1005-configuration-resolution/main/~master/main/source/app.d
deleted file mode 100644
index 0ec7361..0000000
--- a/test/issue1005-configuration-resolution/main/~master/main/source/app.d
+++ /dev/null
@@ -1,6 +0,0 @@
-import b;
-
-void main()
-{
-	foo();
-}
diff --git a/test/issue1024-selective-upgrade.sh b/test/issue1024-selective-upgrade.sh
index ef60333..dc7c009 100755
--- a/test/issue1024-selective-upgrade.sh
+++ b/test/issue1024-selective-upgrade.sh
@@ -2,13 +2,13 @@
 
 . $(dirname "${BASH_SOURCE[0]}")/common.sh
 cd ${CURR_DIR}/issue1024-selective-upgrade
-echo "{\"fileVersion\": 1,\"versions\": {\"a\": \"1.0.0\", \"b\": \"1.0.0\"}}" > main/~master/main/dub.selections.json
-$DUB upgrade --bare --root=main/~master/main/ a
+echo "{\"fileVersion\": 1,\"versions\": {\"a\": \"1.0.0\", \"b\": \"1.0.0\"}}" > main/dub.selections.json
+$DUB upgrade --bare --root=main a
 
-if ! grep -c -e "\"a\": \"1.0.1\"" main/~master/main/dub.selections.json; then
+if ! grep -c -e "\"a\": \"1.0.1\"" main/dub.selections.json; then
 	die $LINENO "Specified dependency was not upgraded."
 fi
 
-if grep -c -e "\"b\": \"1.0.1\"" main/~master/main/dub.selections.json; then
+if grep -c -e "\"b\": \"1.0.1\"" main/dub.selections.json; then
 	die $LINENO "Non-specified dependency got upgraded."
 fi
diff --git a/test/issue1024-selective-upgrade/a-1.0.0/dub.sdl b/test/issue1024-selective-upgrade/a-1.0.0/dub.sdl
new file mode 100644
index 0000000..7ff9fa1
--- /dev/null
+++ b/test/issue1024-selective-upgrade/a-1.0.0/dub.sdl
@@ -0,0 +1,2 @@
+name "a"
+version "1.0.0"
diff --git a/test/issue1024-selective-upgrade/a-1.0.1/dub.sdl b/test/issue1024-selective-upgrade/a-1.0.1/dub.sdl
new file mode 100644
index 0000000..5c8a407
--- /dev/null
+++ b/test/issue1024-selective-upgrade/a-1.0.1/dub.sdl
@@ -0,0 +1,2 @@
+name "a"
+version "1.0.1"
diff --git a/test/issue1024-selective-upgrade/a/1.0.0/a/dub.sdl b/test/issue1024-selective-upgrade/a/1.0.0/a/dub.sdl
deleted file mode 100644
index 7ff9fa1..0000000
--- a/test/issue1024-selective-upgrade/a/1.0.0/a/dub.sdl
+++ /dev/null
@@ -1,2 +0,0 @@
-name "a"
-version "1.0.0"
diff --git a/test/issue1024-selective-upgrade/a/1.0.1/a/dub.sdl b/test/issue1024-selective-upgrade/a/1.0.1/a/dub.sdl
deleted file mode 100644
index 5c8a407..0000000
--- a/test/issue1024-selective-upgrade/a/1.0.1/a/dub.sdl
+++ /dev/null
@@ -1,2 +0,0 @@
-name "a"
-version "1.0.1"
diff --git a/test/issue1024-selective-upgrade/b-1.0.0/dub.sdl b/test/issue1024-selective-upgrade/b-1.0.0/dub.sdl
new file mode 100644
index 0000000..5597559
--- /dev/null
+++ b/test/issue1024-selective-upgrade/b-1.0.0/dub.sdl
@@ -0,0 +1,2 @@
+name "b"
+version "1.0.0"
diff --git a/test/issue1024-selective-upgrade/b-1.0.1/dub.sdl b/test/issue1024-selective-upgrade/b-1.0.1/dub.sdl
new file mode 100644
index 0000000..5e0c01a
--- /dev/null
+++ b/test/issue1024-selective-upgrade/b-1.0.1/dub.sdl
@@ -0,0 +1,2 @@
+name "b"
+version "1.0.1"
diff --git a/test/issue1024-selective-upgrade/b/1.0.0/b/dub.sdl b/test/issue1024-selective-upgrade/b/1.0.0/b/dub.sdl
deleted file mode 100644
index 5597559..0000000
--- a/test/issue1024-selective-upgrade/b/1.0.0/b/dub.sdl
+++ /dev/null
@@ -1,2 +0,0 @@
-name "b"
-version "1.0.0"
diff --git a/test/issue1024-selective-upgrade/b/1.0.1/b/dub.sdl b/test/issue1024-selective-upgrade/b/1.0.1/b/dub.sdl
deleted file mode 100644
index 5e0c01a..0000000
--- a/test/issue1024-selective-upgrade/b/1.0.1/b/dub.sdl
+++ /dev/null
@@ -1,2 +0,0 @@
-name "b"
-version "1.0.1"
diff --git a/test/issue1024-selective-upgrade/main/dub.sdl b/test/issue1024-selective-upgrade/main/dub.sdl
new file mode 100644
index 0000000..a9da177
--- /dev/null
+++ b/test/issue1024-selective-upgrade/main/dub.sdl
@@ -0,0 +1,3 @@
+name "test"
+dependency "a" version="~>1.0.0"
+dependency "b" version="~>1.0.0"
diff --git a/test/issue1024-selective-upgrade/main/~master/main/dub.sdl b/test/issue1024-selective-upgrade/main/~master/main/dub.sdl
deleted file mode 100644
index a9da177..0000000
--- a/test/issue1024-selective-upgrade/main/~master/main/dub.sdl
+++ /dev/null
@@ -1,3 +0,0 @@
-name "test"
-dependency "a" version="~>1.0.0"
-dependency "b" version="~>1.0.0"
diff --git a/test/issue564-invalid-upgrade-dependency.sh b/test/issue564-invalid-upgrade-dependency.sh
index fe1b6a3..19258ce 100755
--- a/test/issue564-invalid-upgrade-dependency.sh
+++ b/test/issue564-invalid-upgrade-dependency.sh
@@ -2,4 +2,7 @@
 
 . $(dirname "${BASH_SOURCE[0]}")/common.sh
 cd ${CURR_DIR}/issue564-invalid-upgrade-dependency
-${DUB} build -f --bare --compiler=${DC} main
+rm -rf a-1.0.0/.dub
+rm -rf a-1.1.0/.dub
+rm -rf main/.dub
+${DUB} build --bare --compiler=${DC} main
diff --git a/test/issue564-invalid-upgrade-dependency/a-1.0.0/dub.json b/test/issue564-invalid-upgrade-dependency/a-1.0.0/dub.json
new file mode 100644
index 0000000..cc36ecb
--- /dev/null
+++ b/test/issue564-invalid-upgrade-dependency/a-1.0.0/dub.json
@@ -0,0 +1,4 @@
+{
+	"name": "a",
+	"version": "1.0.0",
+}
diff --git a/test/issue564-invalid-upgrade-dependency/a-1.0.0/source/a.d b/test/issue564-invalid-upgrade-dependency/a-1.0.0/source/a.d
new file mode 100644
index 0000000..45d8a32
--- /dev/null
+++ b/test/issue564-invalid-upgrade-dependency/a-1.0.0/source/a.d
@@ -0,0 +1,3 @@
+void test()
+{
+}
diff --git a/test/issue564-invalid-upgrade-dependency/a-1.1.0/dub.json b/test/issue564-invalid-upgrade-dependency/a-1.1.0/dub.json
new file mode 100644
index 0000000..4103fe5
--- /dev/null
+++ b/test/issue564-invalid-upgrade-dependency/a-1.1.0/dub.json
@@ -0,0 +1,7 @@
+{
+	"name": "a",
+	"version": "1.1.0",
+	"dependencies": {
+		"invalid": {"path": "invalid"}
+	}
+}
diff --git a/test/issue564-invalid-upgrade-dependency/a-1.1.0/source/a.d b/test/issue564-invalid-upgrade-dependency/a-1.1.0/source/a.d
new file mode 100644
index 0000000..45d8a32
--- /dev/null
+++ b/test/issue564-invalid-upgrade-dependency/a-1.1.0/source/a.d
@@ -0,0 +1,3 @@
+void test()
+{
+}
diff --git a/test/issue564-invalid-upgrade-dependency/a/1.0.0/a/dub.json b/test/issue564-invalid-upgrade-dependency/a/1.0.0/a/dub.json
deleted file mode 100644
index cc36ecb..0000000
--- a/test/issue564-invalid-upgrade-dependency/a/1.0.0/a/dub.json
+++ /dev/null
@@ -1,4 +0,0 @@
-{
-	"name": "a",
-	"version": "1.0.0",
-}
diff --git a/test/issue564-invalid-upgrade-dependency/a/1.0.0/a/source/a.d b/test/issue564-invalid-upgrade-dependency/a/1.0.0/a/source/a.d
deleted file mode 100644
index 45d8a32..0000000
--- a/test/issue564-invalid-upgrade-dependency/a/1.0.0/a/source/a.d
+++ /dev/null
@@ -1,3 +0,0 @@
-void test()
-{
-}
diff --git a/test/issue564-invalid-upgrade-dependency/a/1.1.0/a/dub.json b/test/issue564-invalid-upgrade-dependency/a/1.1.0/a/dub.json
deleted file mode 100644
index 4103fe5..0000000
--- a/test/issue564-invalid-upgrade-dependency/a/1.1.0/a/dub.json
+++ /dev/null
@@ -1,7 +0,0 @@
-{
-	"name": "a",
-	"version": "1.1.0",
-	"dependencies": {
-		"invalid": {"path": "invalid"}
-	}
-}
diff --git a/test/issue564-invalid-upgrade-dependency/a/1.1.0/a/source/a.d b/test/issue564-invalid-upgrade-dependency/a/1.1.0/a/source/a.d
deleted file mode 100644
index 45d8a32..0000000
--- a/test/issue564-invalid-upgrade-dependency/a/1.1.0/a/source/a.d
+++ /dev/null
@@ -1,3 +0,0 @@
-void test()
-{
-}
diff --git a/test/issue564-invalid-upgrade-dependency/main/dub.json b/test/issue564-invalid-upgrade-dependency/main/dub.json
new file mode 100644
index 0000000..7d27d9d
--- /dev/null
+++ b/test/issue564-invalid-upgrade-dependency/main/dub.json
@@ -0,0 +1,6 @@
+{
+	"name": "main",
+	"dependencies": {
+		"a": "~>1.0"
+	}
+}
diff --git a/test/issue564-invalid-upgrade-dependency/main/dub.selections.json b/test/issue564-invalid-upgrade-dependency/main/dub.selections.json
new file mode 100644
index 0000000..e24adfe
--- /dev/null
+++ b/test/issue564-invalid-upgrade-dependency/main/dub.selections.json
@@ -0,0 +1,6 @@
+{
+	"fileVersion": 1,
+	"versions": {
+		"a": "1.0.0"
+	}
+}
diff --git a/test/issue564-invalid-upgrade-dependency/main/source/app.d b/test/issue564-invalid-upgrade-dependency/main/source/app.d
new file mode 100644
index 0000000..b248b89
--- /dev/null
+++ b/test/issue564-invalid-upgrade-dependency/main/source/app.d
@@ -0,0 +1,6 @@
+import a;
+
+void main()
+{
+	test();
+}
diff --git a/test/issue564-invalid-upgrade-dependency/main/~master/main/dub.json b/test/issue564-invalid-upgrade-dependency/main/~master/main/dub.json
deleted file mode 100644
index 7d27d9d..0000000
--- a/test/issue564-invalid-upgrade-dependency/main/~master/main/dub.json
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-	"name": "main",
-	"dependencies": {
-		"a": "~>1.0"
-	}
-}
diff --git a/test/issue564-invalid-upgrade-dependency/main/~master/main/source/app.d b/test/issue564-invalid-upgrade-dependency/main/~master/main/source/app.d
deleted file mode 100644
index b248b89..0000000
--- a/test/issue564-invalid-upgrade-dependency/main/~master/main/source/app.d
+++ /dev/null
@@ -1,6 +0,0 @@
-import a;
-
-void main()
-{
-	test();
-}
diff --git a/test/issue813-pure-sub-dependency.sh b/test/issue813-pure-sub-dependency.sh
index a76dee8..ec2291e 100755
--- a/test/issue813-pure-sub-dependency.sh
+++ b/test/issue813-pure-sub-dependency.sh
@@ -2,5 +2,8 @@
 
 . $(dirname "${BASH_SOURCE[0]}")/common.sh
 cd ${CURR_DIR}/issue813-pure-sub-dependency
-rm -f main/~master/main/dub.selections.json
-${DUB} build -f --bare --compiler=${DC} main
+rm -rf main/.dub
+rm -rf sub/.dub
+rm -rf sub/sub/.dub
+rm -f main/dub.selections.json
+${DUB} build --bare --compiler=${DC} main
diff --git a/test/issue813-pure-sub-dependency/main/dub.sdl b/test/issue813-pure-sub-dependency/main/dub.sdl
new file mode 100644
index 0000000..79f7d71
--- /dev/null
+++ b/test/issue813-pure-sub-dependency/main/dub.sdl
@@ -0,0 +1,3 @@
+name "main"
+targetType "executable"
+dependency "sub:sub" version="*"
diff --git a/test/issue813-pure-sub-dependency/main/src/app.d b/test/issue813-pure-sub-dependency/main/src/app.d
new file mode 100644
index 0000000..0b416f0
--- /dev/null
+++ b/test/issue813-pure-sub-dependency/main/src/app.d
@@ -0,0 +1,6 @@
+import sub.test;
+
+void main()
+{
+	foo();
+}
diff --git a/test/issue813-pure-sub-dependency/main/~master/main/dub.sdl b/test/issue813-pure-sub-dependency/main/~master/main/dub.sdl
deleted file mode 100644
index 79f7d71..0000000
--- a/test/issue813-pure-sub-dependency/main/~master/main/dub.sdl
+++ /dev/null
@@ -1,3 +0,0 @@
-name "main"
-targetType "executable"
-dependency "sub:sub" version="*"
diff --git a/test/issue813-pure-sub-dependency/main/~master/main/src/app.d b/test/issue813-pure-sub-dependency/main/~master/main/src/app.d
deleted file mode 100644
index 0b416f0..0000000
--- a/test/issue813-pure-sub-dependency/main/~master/main/src/app.d
+++ /dev/null
@@ -1,6 +0,0 @@
-import sub.test;
-
-void main()
-{
-	foo();
-}
diff --git a/test/issue813-pure-sub-dependency/sub/dub.sdl b/test/issue813-pure-sub-dependency/sub/dub.sdl
new file mode 100644
index 0000000..f8bdac6
--- /dev/null
+++ b/test/issue813-pure-sub-dependency/sub/dub.sdl
@@ -0,0 +1,3 @@
+name "sub"
+subPackage "sub/"
+dependency ":sub" version="*"
diff --git a/test/issue813-pure-sub-dependency/sub/sub/dub.sdl b/test/issue813-pure-sub-dependency/sub/sub/dub.sdl
new file mode 100644
index 0000000..a932e26
--- /dev/null
+++ b/test/issue813-pure-sub-dependency/sub/sub/dub.sdl
@@ -0,0 +1 @@
+name "sub"
diff --git a/test/issue813-pure-sub-dependency/sub/sub/src/sub/test.d b/test/issue813-pure-sub-dependency/sub/sub/src/sub/test.d
new file mode 100644
index 0000000..fe5bb2c
--- /dev/null
+++ b/test/issue813-pure-sub-dependency/sub/sub/src/sub/test.d
@@ -0,0 +1,6 @@
+module sub.test;
+
+void foo()
+{
+
+}
\ No newline at end of file
diff --git a/test/issue813-pure-sub-dependency/sub/~master/sub/dub.sdl b/test/issue813-pure-sub-dependency/sub/~master/sub/dub.sdl
deleted file mode 100644
index f8bdac6..0000000
--- a/test/issue813-pure-sub-dependency/sub/~master/sub/dub.sdl
+++ /dev/null
@@ -1,3 +0,0 @@
-name "sub"
-subPackage "sub/"
-dependency ":sub" version="*"
diff --git a/test/issue813-pure-sub-dependency/sub/~master/sub/sub/dub.sdl b/test/issue813-pure-sub-dependency/sub/~master/sub/sub/dub.sdl
deleted file mode 100644
index a932e26..0000000
--- a/test/issue813-pure-sub-dependency/sub/~master/sub/sub/dub.sdl
+++ /dev/null
@@ -1 +0,0 @@
-name "sub"
diff --git a/test/issue813-pure-sub-dependency/sub/~master/sub/sub/src/sub/test.d b/test/issue813-pure-sub-dependency/sub/~master/sub/sub/src/sub/test.d
deleted file mode 100644
index fe5bb2c..0000000
--- a/test/issue813-pure-sub-dependency/sub/~master/sub/sub/src/sub/test.d
+++ /dev/null
@@ -1,6 +0,0 @@
-module sub.test;
-
-void foo()
-{
-
-}
\ No newline at end of file
diff --git a/test/issue923-subpackage-deps.sh b/test/issue923-subpackage-deps.sh
index 67e137b..f3be79c 100755
--- a/test/issue923-subpackage-deps.sh
+++ b/test/issue923-subpackage-deps.sh
@@ -2,10 +2,13 @@
 
 . $(dirname "${BASH_SOURCE[0]}")/common.sh
 cd ${CURR_DIR}/issue923-subpackage-deps
-rm -f main/~master/main/dub.selections.json
-${DUB} build -f --bare --compiler=${DC} main
+rm -rf main/.dub
+rm -rf a/.dub
+rm -rf b/.dub
+rm -f main/dub.selections.json
+${DUB} build --bare --compiler=${DC} main
 
 
-if ! grep -c -e \"b\" main/~master/main/dub.selections.json; then
+if ! grep -c -e \"b\" main/dub.selections.json; then
 	die $LINENO 'Dependency b not resolved.'
 fi
diff --git a/test/issue923-subpackage-deps/a/1.0.0/a/dub.sdl b/test/issue923-subpackage-deps/a/1.0.0/a/dub.sdl
deleted file mode 100644
index 259eecf..0000000
--- a/test/issue923-subpackage-deps/a/1.0.0/a/dub.sdl
+++ /dev/null
@@ -1,13 +0,0 @@
-name "a"
-
-dependency ":foo" version="*"
-
-subPackage {
-	name "foo"
-	dependency "b" version="*"
-}
-
-subPackage {
-	name "bar"
-	dependency "a" version="*"
-}
\ No newline at end of file
diff --git a/test/issue923-subpackage-deps/a/dub.sdl b/test/issue923-subpackage-deps/a/dub.sdl
new file mode 100644
index 0000000..259eecf
--- /dev/null
+++ b/test/issue923-subpackage-deps/a/dub.sdl
@@ -0,0 +1,13 @@
+name "a"
+
+dependency ":foo" version="*"
+
+subPackage {
+	name "foo"
+	dependency "b" version="*"
+}
+
+subPackage {
+	name "bar"
+	dependency "a" version="*"
+}
\ No newline at end of file
diff --git a/test/issue923-subpackage-deps/b/1.0.0/b/dub.sdl b/test/issue923-subpackage-deps/b/1.0.0/b/dub.sdl
deleted file mode 100644
index c37c6fc..0000000
--- a/test/issue923-subpackage-deps/b/1.0.0/b/dub.sdl
+++ /dev/null
@@ -1 +0,0 @@
-name "b"
\ No newline at end of file
diff --git a/test/issue923-subpackage-deps/b/1.0.0/b/source/b.d b/test/issue923-subpackage-deps/b/1.0.0/b/source/b.d
deleted file mode 100644
index 5b09673..0000000
--- a/test/issue923-subpackage-deps/b/1.0.0/b/source/b.d
+++ /dev/null
@@ -1,5 +0,0 @@
-module b;
-
-void test()
-{
-}
diff --git a/test/issue923-subpackage-deps/b/dub.sdl b/test/issue923-subpackage-deps/b/dub.sdl
new file mode 100644
index 0000000..c37c6fc
--- /dev/null
+++ b/test/issue923-subpackage-deps/b/dub.sdl
@@ -0,0 +1 @@
+name "b"
\ No newline at end of file
diff --git a/test/issue923-subpackage-deps/b/source/b.d b/test/issue923-subpackage-deps/b/source/b.d
new file mode 100644
index 0000000..5b09673
--- /dev/null
+++ b/test/issue923-subpackage-deps/b/source/b.d
@@ -0,0 +1,5 @@
+module b;
+
+void test()
+{
+}
diff --git a/test/issue923-subpackage-deps/main/dub.sdl b/test/issue923-subpackage-deps/main/dub.sdl
new file mode 100644
index 0000000..42865df
--- /dev/null
+++ b/test/issue923-subpackage-deps/main/dub.sdl
@@ -0,0 +1,2 @@
+name "main"
+dependency "a:bar" version="*"
diff --git a/test/issue923-subpackage-deps/main/source/app.d b/test/issue923-subpackage-deps/main/source/app.d
new file mode 100644
index 0000000..786e416
--- /dev/null
+++ b/test/issue923-subpackage-deps/main/source/app.d
@@ -0,0 +1,6 @@
+import b;
+
+void main()
+{
+	test();
+}
diff --git a/test/issue923-subpackage-deps/main/~master/main/dub.sdl b/test/issue923-subpackage-deps/main/~master/main/dub.sdl
deleted file mode 100644
index 42865df..0000000
--- a/test/issue923-subpackage-deps/main/~master/main/dub.sdl
+++ /dev/null
@@ -1,2 +0,0 @@
-name "main"
-dependency "a:bar" version="*"
diff --git a/test/issue923-subpackage-deps/main/~master/main/source/app.d b/test/issue923-subpackage-deps/main/~master/main/source/app.d
deleted file mode 100644
index 786e416..0000000
--- a/test/issue923-subpackage-deps/main/~master/main/source/app.d
+++ /dev/null
@@ -1,6 +0,0 @@
-import b;
-
-void main()
-{
-	test();
-}