The test script is as follows:

    from PyQt4.QtCore import QFileInfo,QString,QStringList
    from qgis.core import *

    QgsApplication([], False) #initialize the qgis application
    QgsApplication.setPrefixPath("/usr/local", True)
    QgsApplication.initQgis()
    print "Version"
    print QGis.QGIS_VERSION
    print "Settings"
    print QgsApplication.showSettings()
    print "Provider list"
    providers=QgsProviderRegistry.instance().providerList()
    for provider in providers:
        print provider
    proj=QgsProject.instance()
    proj.read(QFileInfo("project.qgs"))
    root = QgsProject.instance().layerTreeRoot()
    layer = QgsVectorLayer("Point", "Layer 1", "memory")
    print layer.isValid()
    print "***Adding layer...***"
    QgsMapLayerRegistry.instance().addMapLayer(layer,True)
    proj.write(QFileInfo("output.qgs"))

And produces the following output:

    Version
    2.6.1-Brighton
    Settings
    Application state:
    QGIS_PREFIX_PATH env var:
    Prefix:     /usr/local
    Plugin Path:        /usr/local/lib/qgis/plugins
    Package Data Path:  /usr/local/share/qgis
    Active Theme Name:
    Active Theme Path:  :/images/themes//
    Default Theme Path: :/images/themes/default/
    SVG Search Paths:   /usr/share/qgis/svg/
            /usr/local/share/qgis/svg/
    User DB Path:   /usr/local/share/qgis/resources/qgis.db

    Provider list
    memory
    (..others omitted...)
    wms
    True
    ***Adding layer...***
    Segmentation fault