Here is a video that captures a manifestation of this issue (and offers evidence that it does indeed exist as I say it does):

http://screencast.com/t/ZmY5MjA2YjQt

This is likely also of interest:

Lein version:

Leiningen 1.2.0 on Java 1.6.0_20 Java HotSpot(TM) 64-Bit Server VM

Lein Jar:

$ ll ~/.m2/repository/leiningen/leiningen/1.2.0/leiningen-1.2.0-standalone.jar
-rw-r--r--  1 timcharper  wheel  6674337 Aug  5 12:25 /Users/timcharper/.m2/repository/leiningen/leiningen/1.2.0/leiningen-1.2.0-standalone.jar

OK... it turns out that it wasn't the fact that I had clj-stacktrace-0.1.2.jar in my lib/dev folder.. I rm'd it and the issue still manifested.

I had compiled fragments of clj-stacktrace, somehow, in my classes folder, and those pieces were taking precedence.

timcharper@timcharper:~/LMP/lt-uber/appraiser production$ ll classes/
total 16
drwxr-xr-x  15 timcharper  staff   510 Jul 28 12:18 clj_stacktrace
drwxr-xr-x   3 timcharper  staff   102 Jul 28 12:18 clojure
-rw-r--r--   1 timcharper  staff  2657 Jul 28 12:18 core$loading__4403__auto__.class
-rw-r--r--   1 timcharper  staff  1732 Jul 28 12:18 core.class
drwxr-xr-x  32 timcharper  staff  1088 Jul 28 12:18 lt
drwxr-xr-x  79 timcharper  staff  2686 Jul 28 12:18 schema_map
drwxr-xr-x  39 timcharper  staff  1326 Jul 28 12:18 somnium
timcharper@timcharper:~/LMP/lt-uber/appraiser production$ ll classes/clj_stacktrace/utils
utils$fence.class                  utils$mash$fn__1689.class          utils$quartile3.class              utils$re_without.class             utils__init.class
utils$high.class                   utils$mash.class                   utils$re_get.class                 utils$rjust.class                  
utils$loading__4403__auto__.class  utils$quartile1.class              utils$re_match_QMARK_.class        utils$zip.class      

when deciding whether to use a compiled class or a new source, it appears like it goes by timestamp. If the clj_stacktrace/utils.clj file is older than the compiled classes, then the compiled files are used. however, if it's newer, then the compiled files aren't used.

Somehow, version 0.1.2 clj_stacktrace/utils.clj was the only file that appears to have compiled remnants.

lein clean deletes my classes folder and would've resolved the issue for me.

In this light, it seems unwise to run lein deps without running lein clean first. A default behavior for lein deps may be to intelligently (or not intelligently) clean the classes folder everytime.

While I totally agree that we need better de-duplication between dependencies and dev-dependencies, the problem you describe with class files has been fixed in Leiningen 1.4.

Excellent news indeed, technomancy. Thank you!

The profiles functionality in 2.0 takes care of this.