I am running Middlegen 2.1 against an older Oracle db(8.x we think), and it drops this error regarding the synonyms in the schema:
$ ant
Buildfile: build.xml

init:

fail-if-no-xdoclet-1.2:

check-driver-present:

panic-if-driver-not-present:

middlegen:
[middlegen] Database
URL:jdbc:oracle:thin:@iddb02.lab.usi.net:1521:XPDWACD1
[middlegen] No <table> elements specified. Reading all tables. This might take a while...

BUILD FAILED
C:\Documents and Settings\#taustin\Desktop\dev downloads\middlegen-2.1\samples\b
uild.xml:228: middlegen.MiddlegenException: Wow! Synonym CDCREDITREQUEST_SN not found. How can it happen?
Configured schema:IWDEV
Configured catalog:
Available schemas:
DBSNMP
IWDEV
OUTLN
PRODQUERY
SYS
SYSTEM
UPDATENOC
Available catalogs:

The Synonyms have valid links, the tables they link to exist and are queryable. Any insights? Is there a command line argument I can use to make middlegen only pull table information?

Oracle synonyms are supported but I have not ever tested them so I am not sure if they still work or not. I suggest you create a bug report in SFs bug tracker system for Middlegen.

Is there a way for me to make middlegen ignore synonyms? Failing the ability to map the synonyms, it would be nice to just have middlegen map the tables in the DB itself, so is there a command line argument I can give it that will make it do a barebones operation on the db (e.g. like reading only tables and views, instead of tripping on fancier features)?

No way to do it at the moment (it is reasonable request so add it to SF bug Tracker). It is easy enough to stop them being selected. Change the isOracle() request in MiddlegenPopulator to return false and it will no longer add them. This is a Hack but it might do what you need.

Alternative, create the option and the lookup code and provide the patch. Its not a big job.

I may just do that, I'll ask my coworkers if this is an allowable use of my worktime(I may do it at home). Either way, I will request the feature on sourceforge.