[R] various R code maintenance

[khotilov]

This PR is to clear a number of long-standing and recently found annoyances and problems.

• Most of functions must work with an xgb.Booster model when it has an invalid handle, e.g., when it was loaded as a regular R object. Also provide users with a function xgb.Booster.complete to restore a missing handle. Relevant: save the model under caret #1955, booster handle is invalid #1958
• Storing the evaluation_log in an xgb.Booster should only depend on the presence of watchlist, but not on verbose value. I've got a number of complaints about this previous side-effect of verbose.
• Reduce the amount of useless printouts from unit tests using this easy verbose=0 switch.
• Windows 64 should still run all the tests.
• Storing feature names of training data with xgb.Booster is useful for bookkeeping and for making further analysis of the model easier.
• Co-occurrence computation was broken for quite awhile, and there was an agreement to get rid of it Variable Importance with co-occurence computation does not work #1092.
• Documentation and tests updates.

I didn't add anything relevant to the new fast histogram updater yet.

[tqchen]

@hetong007 can you help review this?

[codecov-io]

Current coverage is 30.73% (diff: 100%)

Merging #1964 into master will increase coverage by 0.03%

@@             master      #1964   diff @@
==========================================
  Files            72         72          
  Lines          5821       5821          
  Methods         885        885          
  Messages          0          0          
  Branches        580        580          
==========================================
+ Hits           1787       1789     +2   
+ Misses         3956       3955     -1   
+ Partials         78         77     -1   

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[hetong007]

I have reviewed this PR, it seems good to me. Thank you @khotilov .

A meta question, seems new to me, is: How do I "approve" this PR? @tqchen

[tqchen]

@hetong007 https://help.github.com/articles/approving-a-pull-request-with-required-reviews/