Fix a bunch of issues related to checkout in non-root directories

Have to convert file paths to/from cwd-relative and root-relative:
1. cwd->root for include filter arguments (user is in cwd, ls-tree is rooted)
2. root->cwd when writing files & update-index since both are relative to cwd not root like results

commands/command_checkout.go

@@ -21,7 +21,19 @@ var (
 func checkoutCommand(cmd *cobra.Command, args []string) {
 
 	// Parameters are filters
-	checkoutWithIncludeExclude(args, nil)
+	// firstly convert any pathspecs to the root of the repo, in case this is being executed in a sub-folder
+	var rootedpaths = make([]string, len(args))
+	inchan := make(chan string, 1)
+	outchan, err := lfs.ConvertCwdFilesRelativeToRepo(inchan)
+	if err != nil {
+		Panic(err, "Could not checkout")
+	}
+	for _, arg := range args {
+		inchan <- arg
+		rootedpaths = append(rootedpaths, <-outchan)
+	}
+	close(inchan)
+	checkoutWithIncludeExclude(rootedpaths, nil)
 }
 
 func init() {
@@ -78,6 +90,14 @@ func checkoutWithChan(in <-chan *lfs.WrappedPointer) {
 		Panic(err, "Could not update the index")
 	}
 
+	// Get a converter from repo-relative to cwd-relative
+	// Since writing data & calling git update-index must be relative to cwd
+	repopathchan := make(chan string, 1)
+	cwdpathchan, err := lfs.ConvertRepoFilesRelativeToCwd(repopathchan)
+	if err != nil {
+		Panic(err, "Could not convert file paths")
+	}
+
 	// As files come in, write them to the wd and update the index
 	for pointer := range in {
 
@@ -96,13 +116,16 @@ func checkoutWithChan(in <-chan *lfs.WrappedPointer) {
 			continue
 		}
 		// OK now we can (over)write the file content
-		err = lfs.PointerSmudgeToFile(pointer.Name, pointer.Pointer, nil)
+		repopathchan <- pointer.Name
+		cwdfilepath := <-cwdpathchan
+		err = lfs.PointerSmudgeToFile(cwdfilepath, pointer.Pointer, nil)
 		if err != nil {
 			Panic(err, "Could not checkout file")
 		}
 
-		updateIdxStdin.Write([]byte(pointer.Name + "\n"))
+		updateIdxStdin.Write([]byte(cwdfilepath + "\n"))
 	}
+	close(repopathchan)
 
 	updateIdxStdin.Close()
 	if err := cmd.Wait(); err != nil {

lfs/util.go

@@ -173,6 +173,78 @@ func GetPlatform() Platform {
 	return currentPlatform
 }
 
+// Convert filenames expressed relative to the root of the repo relative to the
+// current working dir. Useful when needing to calling git with results from a rooted command,
+// but the user is in a subdir of their repo
+// Pass in a channel which you will fill with relative files & receive a channel which will get results
+func ConvertRepoFilesRelativeToCwd(repochan <-chan string) (<-chan string, error) {
+	wd, err := os.Getwd()
+	if err != nil {
+		return nil, fmt.Errorf("Unable to get working dir: %v", err)
+	}
+
+	// Early-out if working dir is root dir, same result
+	passthrough := false
+	if LocalWorkingDir == wd {
+		passthrough = true
+	}
+
+	outchan := make(chan string, 1)
+
+	go func() {
+		for f := range repochan {
+			if passthrough {
+				outchan <- f
+				continue
+			}
+			abs := filepath.Join(LocalWorkingDir, f)
+			rel, err := filepath.Rel(wd, abs)
+			if err != nil {
+				// Use absolute file instead
+				outchan <- abs
+			} else {
+				outchan <- rel
+			}
+		}
+		close(outchan)
+	}()
+
+	return outchan, nil
+}
+
+// Convert filenames expressed relative to the current directory to be
+// relative to the repo root. Useful when calling git with arguments that requires them
+// to be rooted but the user is in a subdir of their repo & expects to use relative args
+// Pass in a channel which you will fill with relative files & receive a channel which will get results
+func ConvertCwdFilesRelativeToRepo(cwdchan <-chan string) (<-chan string, error) {
+	curdir, err := os.Getwd()
+	if err != nil {
+		return nil, fmt.Errorf("Could not retrieve current directory: %v", err)
+	}
+	outchan := make(chan string, 1)
+	go func() {
+		for p := range cwdchan {
+			var abs string
+			if filepath.IsAbs(p) {
+				abs = p
+			} else {
+				abs = filepath.Join(curdir, p)
+			}
+			reltoroot, err := filepath.Rel(LocalWorkingDir, abs)
+			if err != nil {
+				// Can't do this, use absolute as best fallback
+				outchan <- abs
+			} else {
+				outchan <- reltoroot
+			}
+		}
+		close(outchan)
+	}()
+
+	return outchan, nil
+
+}
+
 // Are we running on Windows? Need to handle some extra path shenanigans
 func IsWindows() bool {
 	return GetPlatform() == PlatformWindows