Merge pull request #248 from jam2767/master

fixed variable names and created download script
updated mirror script for FIA data

Now better supports psql
renmaed to extra.mysql
renamed to mysql
Tweak to make start.model.runs() wait for remote jobs.

When running on geo.bu.edu, the status message 'out' was coming back as character(0). Then nchar(out)>0 evaluates to logical(0) and causes an error. length(out)>0 evaluates to FALSE as desired.
Merge pull request #249 from ryankelly-uiuc/fix_start.model.runs

Tweak to make start.model.runs() wait for remote jobs.
Fixed write.configs.ed.R to use path+prefix to site/pss/css file. Closes gh-242.
Set IED_INIT_MODE=3 in ED2IN templates.

Reasonable workaround to issue gh-243, which has been updated to describe a better permanent solution.
Merge pull request #250 from ryankelly-uiuc/fix_ED2_SFILIN

Fixed write.configs.ed.R to use path+prefix to site file. Closes gh-242.
Merge pull request #251 from ryankelly-uiuc/fix_ED2IN_templates

Set IED_INIT_MODE=3 in ED2IN templates.
Tweak to make trait conversion (e.g. LMA->SLA) less random

Per discussion at gh-245, setting the random seed before doig trait conversion
should prevent re-run of meta-analysis when forceupdate=AUTO (if traits really
haven't changed since last run).
Added warning for non-matching pss/css/site files

ED will still run if pss and css files exist with the same path+prefix
as the site file, but Pecan gives a warning so user knows they aren't
using the css/pss files they specified in settings.
Merge pull request #252 from ryankelly-uiuc/fix_query.trait.data

Tweak to make trait conversion (e.g. LMA->SLA) less random
Merge pull request #254 from ryankelly-uiuc/ED_input.path.check

Added warning for non-matching pss/css/site files
Using same random seed as test.derive.traits.R
Merge pull request #255 from ryankelly-uiuc/fix_horrible_test_failure

Fix previous edit that makes horrible failed test emails go to everyone
modified workflow.R so that it can take the settings file as a command line arguement
Merge branch 'master' of github.com:PecanProject/pecan
Merge pull request #258 from mdietze/master

Modified workflow.R to take settings file as cmd arg
Modified default sample size in query.trait.data functions

take.samples() had different default (10^6) than derive.trait()
and derive.traits() (10000). In addition, only the former was ever used.
Cleaned up to avoid future confusion.