See answers inline:
- the error seems to be too general, essentially it always raises 
JAVA-EXCEPTION no matter what goes wrong (e.g. it the given input is not a 
valid pdf)
I adapted the error msg to be more clear/specific.

- the java stack trace seems to be sent to standard error
Goes to std err.

- Renders the each page of the PDF document as an image. => Renders each page 
of the PDF document as an image.

- the names of the private functions should also adhere to the code conventions 
renderToImages => render-to-images

- make xqdoc failes because the comments seem to contain invalid xml
 user-defined error [err:UE004]: Error processing module zerr:ZXQD0002 - " This 
module provides funtionality to read the text from PDF documents and
 to render PDF documents to images.
 <a href="";>Apache PDFBox</a> library is used to
 implement these functions.
 <br />
 <br />
 <b>Note:</b> Since this module has a Java library dependency a JVM required
 to be installed on the system. For Windows: jvm.dll is required on the system
 path ( usually located in "C:\Program Files\Java\jre6\bin\client".
 <b>Note:<b> For Debian based Linux distributions install PdfBox and FontBox
 packages: sudo apt-get install libpdfbox-java libfontbox-java
": can not parse as XML for xqdoc: loader parsing error: Opening and ending tag 
mismatch: b line 0 and root
; raised at 

- adapt the year in "Copyright 2006-2009 The FLWOR Foundation." in the .xq file 
(and some other files also)

- would it make sense to return one string per page in the pdf instead of one 
big string?
The API doesn't alow it, but I added two more optional options, to insert a 
user defined string at the start and end of each page.

- remove commented out code in read-pdf.cpp

- valgrind shows tons of invalid writes. Why? Are they critical? Is there 
anything we can do?
Jvm always shows in valgrind, even if nothing is done with it. I was careful to 
remove any allocated memory.

- would it make sense to return the images in a streaming fashion (i.e. don't 
create all base64's in a vector)?
No, because it's a push write of all images. And as discussed, optimize only a 
copy in some cases isn't worth the effort.

- encoding each image shouldn't be necessary and will probably we wasted effort 
because the images might be written to a file in their binary form
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