For example, the namespace @clojure.contrib.def@ has metadata for doc and author.

We see this when we load the file directly from source:
<pre>
<code>
tom@goya:~/src/clj$ java -cp clojure/clojure.jar:clojure-contrib/src clojure.lang.Repl
Clojure 1.1.0-alpha-SNAPSHOT
user=> (load "clojure/contrib/def")
nil
user=> (find-ns 'clojure.contrib.def)
#<Namespace clojure.contrib.def>
user=> ^(find-ns 'clojure.contrib.def)
{:author "Stephen C. Gilardi", :doc "def.clj provides variants of def that make including doc strings and\nmaking private definitions more succinct."}
user=>
</code>
</pre>

But if we load the file from the jar where it's been compiled, the metadata is lost:
<pre>
<code>
tom@goya:~/src/clj$ java -cp clojure/clojure.jar:clojure-contrib/clojure-contrib.jar clojure.lang.Repl
Clojure 1.1.0-alpha-SNAPSHOT
user=> (use 'clojure.contrib.def)
nil
user=> (find-ns 'clojure.contrib.def)
#<Namespace clojure.contrib.def>
user=> ^(find-ns 'clojure.contrib.def)
nil
user=>
</code>
</pre>

Even if we use @load@, we don't see metadata on the item:
<pre>
<code>
tom@goya:~/src/clj$ java -cp clojure/clojure.jar:clojure-contrib/clojure-contrib.jar clojure.lang.Repl
Clojure 1.1.0-alpha-SNAPSHOT
user=> (load "clojure/contrib/def")
nil
user=> (find-ns 'clojure.contrib.def)
#<Namespace clojure.contrib.def>
user=> ^(find-ns 'clojure.contrib.def)
nil
user=>
</code>
</pre>

The jar isn't the problem, for if we use the slim jar (without the AOT
class files), we see that the metadata is fine:
<pre>
<code>
tom@goya:~/src/clj$ java -cp clojure/clojure.jar:clojure-contrib/clojure-contrib-slim.jar clojure.lang.Repl
Clojure 1.1.0-alpha-SNAPSHOT
user=> (use 'clojure.contrib.def)
nil
user=> (find-ns 'clojure.contrib.def)
#<Namespace clojure.contrib.def>
user=> ^(find-ns 'clojure.contrib.def)
{:author "Stephen C. Gilardi", :doc "def.clj provides variants of def that make including doc strings and\nmaking private definitions more succinct."}
user=>
</code>
</pre>

This seems to be true usually, but not always. For example the
metadata on the pretty print namespace is just fine from the AOT version:
<pre>
<code>
tom@goya:~/src/clj$ java -cp clojure/clojure.jar:clojure-contrib/clojure-contrib.jar clojure.lang.Repl
Clojure 1.1.0-alpha-SNAPSHOT
user=> (use 'clojure.contrib.pprint)
nil
user=> (find-ns 'clojure.contrib.pprint)
#<Namespace clojure.contrib.pprint>
user=> ^(find-ns 'clojure.contrib.pprint)
{:author "Tom Faulhaber", :doc "This module comprises two elements:\n1) A pretty printer for Clojure data structures, implemented in the function \"pprint\"\n2) A Common Lisp compatible format function, implemented as \"cl-format\" because\n Clojure is using the name \"format\" for its own format.\n\nComplete documentation is available on the wiki at the contrib google code site.", :see-also [["PrettyPrinting" "Documentation for the pretty printer"] ["CommonLispFormat" "Documentation for Common Lisp format function"]]}
user=>
</code>
</pre>