JSONAlchemy: bug fixes

NOTE: beware, patch amended by Tibor to use new file names
deposit: migrate workflows and fix test

* Migrates existing workflow to new workflow tasks.

* Fixes an issue with a test.

Signed-off-by: Lars Holm Nielsen <lars.holm.nielsen@cern.ch>

NOTE: beware, patch amended by Tibor to use new file names
installation: version modification to 1.9999

Signed-off-by: Jiri Kuncar <jiri.kuncar@cern.ch>

NOTE: beware, patch amended by Tibor to use new file names
installation: MANIFEST.in file recursive-include fix

NOTE: beware, patch amended by Tibor to use new file names
requirements: better separation

* Moves PIL and qrcode to separate requirements file as they are needed together
for formatting records;
* Removes iPython from -extras as it is already included in -dev.

Signed-off-by: Adrian-Tudor Panescu <adrian.tudor.panescu@cern.ch>

NOTE: beware, patch amended by Tibor to use new file names
comments: fix for JavaScript in record tab

* Moves modal binding to separate function in invenio.js;
* Adds macros for injecting CSS and JS.

Signed-off-by: Adrian-Tudor Panescu <adrian.tudor.panescu@cern.ch>

NOTE: beware, patch amended by Tibor to use new file names
deposit: static file fixes

* Added missing plupload to Bower and Grunt;
* Fixed wrong location of jQuery UI themes.

Signed-off-by: Adrian-Tudor Panescu <adrian.tudor.panescu@cern.ch>

NOTE: beware, patch amended by Tibor to use new file names
comments: bind modal on record tab change

Signed-off-by: Adrian-Tudor Panescu <adrian.tudor.panescu@cern.ch>

NOTE: beware, patch amended by Tibor to use new file names
base: add inveniomanage database diff command

* Adds command to diff database schema against installed
  database models.

NOTE: beware, patch amended by Tibor to use new file names
upgrader: change to module-aware engine

* Changes upgrader to load upgrades from all installed modules.

* Changes upgrade naming convention to be compatible with
  invenio modules.

* Changes upgrader to use SQLAlchemy models for querying
  instead of run_sql.

* Changes recipe creation to use module import paths as input
  instead of system paths.

* Relaxes constraint on cross-graph dependencies to allow
  inter-module dependencies.

* Removes pre-upgrade check for legacy custom templates.

* Adds tests of recipe creation.

* Fixes PEP8 issues.

Signed-off-by: Lars Holm Nielsen <lars.holm.nielsen@cern.ch>

NOTE: beware, patch amended by Tibor to use new file names
requirements: qrcode removal

* qrcode removed from main requirements;

Signed-off-by: Adrian-Tudor Panescu <adrian.tudor.panescu@cern.ch>

NOTE: beware, patch amended by Tibor to use new file names
Grunt: typeahead.js fix

Signed-off-by: Adrian-Tudor Panescu <adrian.tudor.panescu@cern.ch>

NOTE: beware, patch amended by Tibor to use new file names
restful: fix extension initialization

Signed-off-by: Jiri Kuncar <jiri.kuncar@cern.ch>

NOTE: beware, patch amended by Tibor to use new file names
deposit: plupload filetable fix

* Displays uploaded files in deposition form.

Signed-off-by: Adrian-Tudor Panescu <adrian.tudor.panescu@cern.ch>

NOTE: beware, patch amended by Tibor to use new file names
upgrader: add auto-generation of upgrades

* Adds auto-generation of upgrades via Alembic.

* Adds dependency on Alembic to perform database schema
  operations.

* Refactors code structure by splitting engine module into
  separate modules.

Signed-off-by: Lars Holm Nielsen <lars.holm.nielsen@cern.ch>

NOTE: beware, patch amended by Tibor to use new file names
upgrader: fix auto-generation of upgrades

* Fixes an issue with wrong upgrades being generated
  due to all SQLAlchemy models not being loaded.

* Adds option to create recipe command to overwrite the
  upgrade file if it already exists, as well as naming it
  from the CLI.

* Fixes an relative import bug in pre/post checks.

Signed-off-by: Lars Holm Nielsen <lars.holm.nielsen@cern.ch>

NOTE: beware, patch amended by Tibor to use new file names
JSONAlchemy: bug fixes and tests improvements

Signed-off-by: Esteban J. G. Gabancho <esteban.gabancho@gmail.com>

NOTE: beware, patch amended by Tibor to use new file names
classifer: fix classifer registry name

* Fixes the name of the classifer registry which accidentially
  was discovered by bibconvert registry due to name clash.

Signed-off-by: Lars Holm Nielsen <lars.holm.nielsen@cern.ch>
Tested-by: Jiri Kuncar <jiri.kuncar@cern.ch>
BibDocFile: hotfix plugins loading

Signed-off-by: Jiri Kuncar <jiri.kuncar@cern.ch>
oairepository: automatically compute model field

* Connects OaiREPOSITORY model to SQLAlchemy events to ensure field
  setDefinition is properly computed on db insert/update when using
  the SQLAlchemy model.