Hi Ben,

Here is a more complete list of tables that may store paths. Some, like those in the ms2 schema, likely don't have any data for your installation.

core.mappeddirectories (filesets)
exp.data (files referenced by assays, uploaded through the file management tool, etc)
exp.experimentrun (directory assay runs came from)
filecontent.fileroots (non-pipeline file roots)
genotyping.analyses (genotyping analyses)
genotyping.runs (genotyping runs)
ms1.files (path to MS1 mzXML files)
ms2.fractions (path to MS2 mzXML files)
ms2.runs (path to MS2 pepXML analysis results)
ms2.proteinprophetfiles (path to MS2 protXML analysis results)
pipeline.pipelineroots (pipeline roots, separate from file roots)
pipeline.statusfiles (log file for pipeline jobs)
prot.annotinserts (path to imported FASTA and SwissProt XML files)
prot.fastafiles (path to imported FASTA files)
prot.fastaloads (history of FASTA imports)
study.uploadlog (history of study loads)

It's possible that I missed a couple, but that should be pretty thorough.

I'll let Brian weigh in on tradeoffs between symlinks and database editing.

Thanks,
Josh