Delete overlays when clearing REPL buffer

Author: rfkm

CHANGELOG.md

@@ -14,6 +14,7 @@
 * [#1479](https://github.com/clojure-emacs/cider/pull/1479): Make paredit and `cider-repl-mode` play nice.
 * [#1452](https://github.com/clojure-emacs/cider/issues/1452): Prevent ANSI color overlays in the REPL buffer from being extended.
 * [#1486](https://github.com/clojure-emacs/cider/issues/1486): Complete a partial fix in stacktrace font-locking.
+* [#1488](https://github.com/clojure-emacs/cider/pull/1488): Delete zombie overlays in the REPL buffer.
 
 ## 0.10.0 / 2015-12-03
 

cider-repl.el

@@ -743,12 +743,17 @@ text property `cider-old-input'."
 
 (defvar cider-repl-clear-buffer-hook)
 
+(defun cider-repl--clear-region (start end)
+  "Delete the output and its overlays between START and END."
+  (mapc 'delete-overlay (overlays-in start end))
+  (delete-region start end))
+
 (defun cider-repl-clear-buffer ()
   "Delete the output generated by the Clojure process."
   (interactive)
   (let ((inhibit-read-only t))
-    (delete-region (point-min) cider-repl-prompt-start-mark)
-    (delete-region cider-repl-output-start cider-repl-output-end)
+    (cider-repl--clear-region (point-min) cider-repl-prompt-start-mark)
+    (cider-repl--clear-region cider-repl-output-start cider-repl-output-end)
     (when (< (point) cider-repl-input-start-mark)
       (goto-char cider-repl-input-start-mark))
     (recenter t))
@@ -773,7 +778,7 @@ With a prefix argument CLEAR-REPL it will clear the entire REPL buffer instead."
           (end (cider-repl--end-of-line-before-input-start)))
       (when (< start end)
         (let ((inhibit-read-only t))
-          (delete-region start end)
+          (cider-repl--clear-region start end)
           (save-excursion
             (goto-char start)
             (insert