Add Permissions to manifest (required for webstart)

Also added Codebase (currently * allows running from anaywhere) and Application-Name (displayed in the webstart dialog, instead of the user-unfriendly classname)
Exit quickly if files are inappropriately added

When using `--wait_completed` and `--close_completed`,
no files are accepted on the command-line. Rather than
silently ignore them, this commit now exits with an ERROR.

```
($ bin/omero import -- --close_completed foo bar
 INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.0-rc1-DEV-ice35
 INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.0-rc1-DEV-ice35 revision: 92e346e date: 6 February 2014
 INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
 ERROR  formats.importer.cli.CommandLineImporter - Files found with completed option: [foo, bar]
```
Change signjar task to apply/exec jarsigner with custom args

The ant signjar task doesn't support -storepass:file.
Note this no longer preserves the original file modification time.
Replace jarsign.storepass property with jarsign.storepassfile

Added default password file lib/keystore.passwd
Replace genkey task with exec keytool -genkey

Need to use -storepass:file
Add jarsigner timestamping
Set default timestamping authority to http://time.certum.pl
Separate PluginLoggerImpl from LoggerImpl

Since all methods in LoggerImpl were checking
`if (runAsPlugin < 0) {...}` separating out the logic
into a separate class is straight-forward. The reason
for doing this, however, is that in the case that the
IJ plugin is used with the `loci_tools.jar` jar, which
contains log4j, then the client hangs at

    "Loading Logger Service"
Use old/new taks depending on whether jarsign.storepassfile is set

Restore old signjar/genkey tasks for Java<1.7
Use the new exec invocation with -storepass:file only if property jarsign.storepassfile is explcitly set
Revert "Replace jarsign.storepass property with jarsign.storepassfile"

This reverts commit 94b0f13505aee0e061d374a65b1b63d55da4e0b2.
Add commented out note about jarsign.storepassfile
Add tsaurl to old signjar tasks
Move jarsign into a new macrodef, echo jar name when signing
Fix header of PluginLoggerImpl
Migrating new advanced help from internal discussion
Remove short-options for transfer
Hide --transfer option from import.py
Merge pull request #2069 from manics/insight_manifest_perms-11772

Insight manifest changes for webstart #11772
Merge pull request #2075 from joshmoore/plugin-logger-impl

Separate PluginLoggerImpl from LoggerImpl
Merge pull request #2071 from joshmoore/final-inplace-fixes

Final in-place fixes