NGI pipeline server finally working

So, this is the first working version for the NGI pipeline server. This PR fixes some opened issues (and removes some old doc). My test has been:

* In nestor (for the moment under my account), the server is running with `ngi_pipeline_start.py server --port 666`
* From `preproc1.scilifelab.se`, I have executed: `curl -X GET http://nestor1.uppmax.uu.se:6666/flowcell_analysis/130611_SN7001298_0148_AH0CCVADXX`, which is a flowcell in `/proj/a2014205/INBOX`

Immediately after that, the tornado server in nestor started the analysis :-) 

```
2014-12-05 16:01:21,084 - ngi_pipeline_start - INFO - Starting flowcell analysis in directory 130611_SN7001298_0148_AH0CCVADXX
2014-12-05 16:01:21,089 - ngi_pipeline.conductor.flowcell - INFO - Setting up analysis for demultiplexed data in source folder "130611_SN7001298_0148_AH0CCVADXX"
2014-12-05 16:01:21,116 - ngi_pipeline.conductor.flowcell - INFO - Parsing flowcell directory "/proj/a2014205/INBOX/130611_SN7001298_0148_AH0CCVADXX"...
2014-12-05 16:01:21,194 - ngi_pipeline.conductor.flowcell - INFO - Parsing project directory "130611_SN7001298_0148_AH0CCVADXX/Unaligned_7bp/Project_A__Wedell_13_03"...
2014-12-05 16:01:21,196 - ngi_pipeline.conductor.flowcell - INFO - Parsing samples directory "130611_SN7001298_0148_AH0CCVADXX/Unaligned_7bp/Project_A__Wedell_13_03/Sample_P567_101"...
2014-12-05 16:01:21,407 - ngi_pipeline.conductor.flowcell - INFO - Setting up project A.Wedell_13_03
2014-12-05 16:01:21,410 - ngi_pipeline.conductor.flowcell - INFO - Setting up sample P567_101
2014-12-05 16:01:21,679 - ngi_pipeline.conductor.flowcell - INFO - Copying fastq files from /proj/a2014205/INBOX/130611_SN7001298_0148_AH0CCVADXX/Unaligned_7bp/Project_A__Wedell_13_03/Sample_P567_101 to /proj/a2014205/INBOX/DATA/P567/P567_101/A/130611_SN7001298_0148_AH0CCVADXX...
2014-12-05 16:01:21,701 - ngi_pipeline.engines.piper_ngi.local_process_tracking - INFO - Updating Charon with the status of all locally-tracked jobs...
2014-12-05 16:01:21,701 - ngi_pipeline.engines.piper_ngi.local_process_tracking - INFO - Updating Charon with the status of all locally-tracked jobs...
2014-12-05 16:01:21,708 - ngi_pipeline.engines.piper_ngi.database - INFO - Creating local job tracking database "//home/guilc/.ngipipeline/record_tracking_database"
2014-12-05 16:01:21,708 - ngi_pipeline.engines.piper_ngi.database - INFO - Creating local job tracking database "//home/guilc/.ngipipeline/record_tracking_database"
...
```

(and after that it crashed because I don't have the pipeline correctly configured, but should be fine)