This mentions the ade4 package, and factominer
The factorminer package also does mca
I think this is the reference that might be the origin of PCA w/ categorical variables in ecology related fields
Hill & Smith 1976 Principal component analysis of taxonomic data with multistate discrete characters
The package ade4 has a function dudi.mca() for multiple correspondence analysis (PCA w/categorical variables) and dudi.hillsmith() which allows you to do a mix; its probably similar to that PCAmix package I sent. ade4 is part of a suite of packages by crazy French ecologists that are REALLY into multivariate stuff- I find most of the documentation really hard to understand (lots of math, not much ecology, not perfect English). They have a paper “The ade4 package: implementing the duality diagram for ecologists” In the Journal for Statistical Software which has a section “4. An example: dudi.hillsmith” where they analyze the “dune meadow” dataset that shows up often in vegan I think. This example, whether analyzed with dudi.hillmsith or the functions in the PCAmix package (or whatever its name is) might be a good place to start.