Merge pull request #145 from HazyResearch/hotfix-weight-table

Hotfix weight table, writeback, chunking test
paleo doc
Merge pull request #149 from HazyResearch/ce_

Ce paleo
Merge pull request #148 from HazyResearch/ce_

paleo doc
broken links
Merge pull request #150 from HazyResearch/ce_

broken links
Merge pull request #151 from HazyResearch/ce_

broken links
Added -N option in mysql execution

-N skips the column header and help exports clean tsv data with --silent.
Do not require deepdive to run in DEEPDIVE_HOME

- Developers can specify environment variable DEEPDIVE_HOME and run
deepdive anywhere. If not specified, deepdive will treat current
directory to be DEEPDIVE_HOME (which is backward compatible)
Use user.dir instead of '.'; Added docs for DEEPDIVE_HOME
Merge branch 'hotfix-ddhome' into develop
Handle known JDBC bug
Fix comment
Merge pull request #155 from HazyResearch/hotfix-jdbcoverflow

Handle known JDBC bug
Throw exception when temporary bash scripts fail
Merge branch 'develop' into zifei-mariadb

- Resolved conflicts
- Try to improve spouse example performance by changing to int IDs and materializing views; not help much

Conflicts:
	src/main/scala/org/deepdive/Context.scala
	src/main/scala/org/deepdive/datastore/Dataloader.scala
	src/main/scala/org/deepdive/extraction/ExtractorRunner.scala
	src/main/scala/org/deepdive/inference/datastore/SQLInferenceDataStore.scala
	src/main/scala/org/deepdive/settings/SettingsParser.scala
Fixed an output bug in helper script
Optimize mysql joins by materializing and indexing

- optimize spouse example with creating indexes that speed up joins
- fixed inference and calibration in DeepDive: for queries with joins,
  create indexes on columns that appear in join conditions. (only for
  mysql)