Use latexmk in Makefile.

.latexmkrc

@@ -0,0 +1,9 @@
+# From https://tex.stackexchange.com/questions/58963/latexmk-with-makeglossaries-and-auxdir-and-outdir#59098
+add_cus_dep('glo', 'gls', 0, 'makeglossaries');
+sub makeglossaries {
+  my ($base_name, $path) = fileparse($_[0]);
+  pushd $path;
+  my $return = system "makeglossaries $base_name";
+  popd;
+  return $return;
+}

Makefile

@@ -1,13 +1,11 @@
 FILE := main
 OUT  := build
 
-all:
-	mkdir -p $(OUT)
-	pdflatex -output-directory $(OUT) $(FILE)
-	biber $(OUT)/$(FILE)
-	cd $(OUT) && makeglossaries $(FILE)
-	pdflatex -output-directory $(OUT) $(FILE)
-	pdflatex -output-directory $(OUT) $(FILE)
+latexmk:
+	# Also see .latexmkrc
+	latexmk -outdir=$(OUT) -pdf $(FILE)
 
 clean:
 	rm -rf $(OUT)
+
+.PHONY: latexmk clean

README.md

@@ -14,7 +14,7 @@ Comments & contributions welcome!
    * Download the TUM logo from [here][mytum-logo-tum] and save it to `logos/tum.pdf`.
    * Download your faculty's logo from [here][mytum-logo-faculty] and save it to `logos/faculty.pdf`.
    * Some logos might not be cropped; execute the `crop-logos` script to do that for you.
- * Configure your latex editor to use `pdflatex`, `biber` for bibliography, and `makeglossaries` for glossary generation. Set `main.tex` as the master document. Alternatively, you can use the provided makefile to create a PDF in the `build` directory.
+ * Configure your latex editor to use `pdflatex`, `biber` for bibliography, and `makeglossaries` for glossary generation. Set `main.tex` as the master document. Alternatively, you can use the provided makefile to create a PDF in the `build` directory (requires `latexmk`).
  * Look for `TODO` comments in the provided files. Start at `main.tex`.
 
 For additional hints, have a look at [the wiki][wiki].