PackageManager: Store packages hierarchically, by version

As explained in the changelog, this hierarchy makes much more sense
than the current one, and will make it possible to read the version
from the directory name.

changelog/hierarchy.dd

@@ -0,0 +1,14 @@
+The way packages are stored internally has changed
+
+Previous versions of dub stored packages in the following format:
+`$CACHE_PATH/$PACKAGE_NAME-$PACKAGE_VERSION/$PACKAGE_NAME/`
+Starting from this version, the format will be:
+`$CACHE_PATH/$PACKAGE_NAME/$PACKAGE_VERSION/$PACKAGE_NAME`.
+
+Introducing a new level will help users quickly list what packages
+they actually have installed, and reduce visibility of packages that
+might update frequently. It will render various commands (e.g. `du`)
+more useful, and pave the way for a package GC function.
+More importantly, it will allow future version of dub to infer the
+version from the path to the package, removing the need to read (or edit)
+the recipe file on every dub invocation.

source/dub/packagemanager.d

@@ -1298,29 +1298,8 @@ private struct Location {
 		if (!path.existsDirectory())
 			return;
 
-		logDebug("iterating dir %s", path.toNativeString());
-		try foreach (pdir; iterateDirectory(path)) {
-			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/`
-			auto pack_path = path ~ (pdir.name ~ "/");
-			auto packageFile = Package.findPackageFile(pack_path);
-
-			// New (since 2015) managed structure:
-			// $ROOT/$NAME-$VERSION/$NAME
-			// This is the most common code path
-			if (mgr.isManagedPath(path) && packageFile.empty) {
-				foreach (subdir; iterateDirectory(path ~ (pdir.name ~ "/")))
-					if (subdir.isDirectory && pdir.name.startsWith(subdir.name)) {
-						pack_path ~= subdir.name ~ "/";
-						packageFile = Package.findPackageFile(pack_path);
-						break;
-					}
-			}
-
-			if (packageFile.empty) continue;
+		void loadInternal (NativePath pack_path, NativePath packageFile)
+		{
 			Package p;
 			try {
 				foreach (pp; existing_packages)
@@ -1338,6 +1317,38 @@ private struct Location {
 				logDiagnostic("Full error: %s", e.toString().sanitize());
 			}
 		}
+
+		logDebug("iterating dir %s", path.toNativeString());
+		try foreach (pdir; iterateDirectory(path)) {
+			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
+			if (mgr.isManagedPath(path) && packageFile.empty) {
+				// Iterate over versions of a package
+				foreach (versdir; iterateDirectory(pack_path)) {
+					if (!versdir.isDirectory) continue;
+					auto vers_path = pack_path ~ versdir.name ~ (pdir.name ~ "/");
+					if (!vers_path.existsDirectory()) continue;
+					packageFile = Package.findPackageFile(vers_path);
+					loadInternal(vers_path, packageFile);
+				}
+			}
+		}
 		catch (Exception e)
 			logDiagnostic("Failed to enumerate %s packages: %s", path.toNativeString(), e.toString());
 	}
@@ -1417,9 +1428,7 @@ private struct Location {
 	 */
 	private NativePath getPackagePath (string name, string vers)
 	{
-		// + has special meaning for Optlink
-		string clean_vers = vers.chompPrefix("~").replace("+", "_");
-		NativePath result = this.packagePath ~ (name ~ "-" ~ clean_vers);
+		NativePath result = this.packagePath ~ name ~ vers;
 		result.endsWithSlash = true;
 		return result;
 	}