[WIP] Start implementation of proper root package patching, extend docs

Author: pinkeen

README.md

@@ -27,9 +27,14 @@ It's (kind-of) an alternative to two other great plugins (differences will becom
 | PHP Version Support confirmed by tests                    | 5.6+                                      | 5.3+                           | no information                      |
 | Apply patches directly from remote locations              | no (no support planned)                   | yes                            | yes                                 |
 | Specify target package version constraints                | yes                                       | no                             | yes                                 |
-| Uninstall removed patches in all cases                    | yes                                       | no                             | TBD                                 |
+| Uninstall removed patches in all cases<sup>1</sup>        | yes                                      | no                             | TBD                                 |
 | Reapply package patches if order has changed              | yes                                       | TBD                            | TBD                                 |
 | Choose application method (git/patch) per patch           | yes                                       | TBD                            | TBD                                 |
+| Apply patches to root package/directory                   | yes                                       | no                             | TBD                                 |
+
+<small>
+    <sup>1</sup> Root package patching is the exception, please see [Applying patches to root package]() in usage docs section.
+</small>
 
 ### Some feature hilights
 
@@ -85,6 +90,18 @@ plugins have done their work so patching source files in vendor will have no eff
 
 ### Define patches in your root package
 
+### Applying patches to root package (root project folder)
+
+Define patches as you normally would. If your root package is not named the you should use special
+`__root__` as package name.
+
+**CAUTION** Since root package cannot be reinstalled once patches are applied they cannot be removed!
+This means that if you want to remove patches applied to root package you should reinstall the whole
+project manually. The plugin will warn you when this is the case but will not fail. It will try
+to apply any new root package patches though.
+
+__New patches will be applied to the root package but then _application order_ is not guaranteed.__
+
 ### Options
 
 #### Strip defined number of components when applying patch (`-pX`)

src/PatchApplication.php

@@ -31,7 +31,7 @@ class PatchApplication
 
     /**
      * @param Patch $patch
-     * @param PackageInterface $sourcePackage
+     * @param PackageInterface|null $sourcePackage
      * @param PackageInterface $targetPackage
      * @param string $hash
      */

src/Patcher.php

@@ -254,6 +254,15 @@ private function reinstallPackages()
         $localRepo = $this->repositoryManager->getLocalRepository();
 
         foreach ($this->packagesToReinstall as $package) {
+            if ($package instanceof RootPackageInterface) {
+                $this->logger->warning(sprintf('Root package patches have changed but cannot reinstall it, will apply only new patches. You should reinstall the whole project to be safe.',
+                    $package->getName(),
+                    $package->getPrettyVersion()
+                ));
+
+                continue;
+            }
+
             $this->logger->notice(sprintf('Reinstalling <info>%s</info> (<comment>%s</comment>) for re-patch',
                 $package->getName(),
                 $package->getPrettyVersion()
@@ -293,6 +302,16 @@ private function applyPatches()
         }
     }
 
+    private function applyPatchesToPackage(PackagePatchApplication $packagePatchApplication)
+    {
+
+    }
+
+    private function applyPatchesToRootPackage(PackagePatchApplication $packagePatchApplication)
+    {
+
+    }
+
     /**
      * @return PackageInterface[]
      */