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project fails to load after I used git to update nrf9160 SDK from 1.0.0 to 1.1.0

I am using windows 10 and have been able to work with the FOTA sample for the nrf9160 for several months.

I needed to update the SDK from 1.0.0 to 1.1.0. I followed the instructions in the nrfConnect tool including

updating to the latest version of the compiler. 

I get the following in the output window in SES. I get a similar error when I try to load in the ble_gateway project

Loading solution aws_fota.emProject
Executing load commands
cmake -GNinja -DBOARD=nrf9160_pca10090ns -DBOARD_DIR=C:/Projects/PCDWorks/nRF9160/ncs/zephyr/boards/arm/nrf9160_pca10090 -DZEPHYR_TOOLCHAIN_VARIANT=gnuarmemb -DGNUARMEMB_TOOLCHAIN_PATH=C:/gnuarmemb -BC:/Projects/PCDWorks/nRF9160/ncs/nrf/samples/nrf9160/aws_fota/build_nrf9160_pca10090ns -HC:/Projects/PCDWorks/nRF9160/ncs/nrf/samples/nrf9160/aws_fota -DEXTRA_KCONFIG_TARGETS=menuconfig_ses -DEXTRA_KCONFIG_TARGET_COMMAND_FOR_menuconfig_ses=C:/Program Files/SEGGER/arm_segger_embedded_studio_v430c_win_x64_nordic/html/configure_nordic_project_menuconfig.py
-- Using application from 'C:/Projects/PCDWorks/nRF9160/ncs/nrf/samples/nrf9160/aws_fota'
Zephyr version: 1.14.99
-- Selected BOARD nrf9160_pca10090ns
-- Found west: C:/Python37/Scripts/west.exe (found suitable version "0.5.8", minimum required is "0.5.6")
validation.invalid
 --- All found errors ---
["Key 'repo-path' was not defined. Path: '/projects/0'", "Key 'repo-path' was not defined. Path: '/projects/3'", "Key 'repo-path' was not defined. Path: '/projects/4'", "Key 'repo-path' was not defined. Path: '/projects/5'", "Key 'repo-path' was not defined. Path: '/projects/6'", "Key 'repo-path' was not defined. Path: '/projects/12'"]
Traceback (most recent call last):
  File "C:\Projects\PCDWorks\nRF9160\ncs\.west\west\src\west\manifest.py", line 153, in __init__
    schema_files=[_SCHEMA_PATH[key]]
  File "c:\python37\lib\site-packages\pykwalify\core.py", line 167, in validate
    error_msg=u'.\n - '.join(self.validation_errors)))
pykwalify.errors.SchemaError: <SchemaError: error code 2: Schema validation failed:
 - Key 'repo-path' was not defined. Path: '/projects/0'.
 - Key 'repo-path' was not defined. Path: '/projects/3'.
 - Key 'repo-path' was not defined. Path: '/projects/4'.
 - Key 'repo-path' was not defined. Path: '/projects/5'.
 - Key 'repo-path' was not defined. Path: '/projects/6'.
 - Key 'repo-path' was not defined. Path: '/projects/12'.: Path: '/'>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
  File "c:\python37\lib\runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "c:\python37\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "C:\Python37\Scripts\west.exe\__main__.py", line 9, in <module>
  File "c:\python37\lib\site-packages\west\_bootstrap\main.py", line 499, in main
    wrap(wrap_argv)
  File "c:\python37\lib\site-packages\west\_bootstrap\main.py", line 485, in wrap
    west.main.main(argv)
  File "C:\Projects\PCDWorks\nRF9160\ncs\.west\west\src\west\main.py", line 569, in main
    extensions = get_extension_commands()
  File "C:\Projects\PCDWorks\nRF9160\ncs\.west\west\src\west\main.py", line 531, in get_extension_commands
    extensions = extension_commands()
  File "C:\Projects\PCDWorks\nRF9160\ncs\.west\west\src\west\commands\command.py", line 181, in extension_commands
    manifest = Manifest.from_file()
  File "C:\Projects\PCDWorks\nRF9160\ncs\.west\west\src\west\manifest.py", line 91, in from_file
    return Manifest(source_file=source_file, sections=sections)
  File "C:\Projects\PCDWorks\nRF9160\ncs\.west\west\src\west\manifest.py", line 156, in __init__
    self._malformed(e, key)
  File "C:\Projects\PCDWorks\nRF9160\ncs\.west\west\src\west\manifest.py", line 226, in _malformed
    complaint))
west.manifest.MalformedManifest: Malformed manifest file C:\Projects\PCDWorks\nRF9160\ncs\nrf\west.yml (schema: C:\Projects\PCDWorks\nRF9160\ncs\.west\west\src\west\manifest-schema.yml):
<SchemaError: error code 2: Schema validation failed:
 - Key 'repo-path' was not defined. Path: '/projects/0'.
 - Key 'repo-path' was not defined. Path: '/projects/3'.
 - Key 'repo-path' was not defined. Path: '/projects/4'.
 - Key 'repo-path' was not defined. Path: '/projects/5'.
 - Key 'repo-path' was not defined. Path: '/projects/6'.
 - Key 'repo-path' was not defined. Path: '/projects/12'.: Path: '/'>

CMake Error at C:/Projects/PCDWorks/nRF9160/ncs/zephyr/cmake/zephyr_module.cmake:45 (message):
  Traceback (most recent call last):
    File "C:/Projects/PCDWorks/nRF9160/ncs/zephyr/scripts/zephyr_module.py", line 168, in <module>
      main()
    File "C:/Projects/PCDWorks/nRF9160/ncs/zephyr/scripts/zephyr_module.py", line 142, in main
      returncode=p.returncode)
  subprocess.CalledProcessError: Command '['C:/Python37/Scripts/west.exe',
  'list', '--format={posixpath}']' returned non-zero exit status 1.
Call Stack (most recent call first):
  C:/Projects/PCDWorks/nRF9160/ncs/zephyr/cmake/app/boilerplate.cmake:249 (include)
  CMakeLists.txt:10 (include)

-- Configuring incomplete, errors occurred!
Project load failed
Reported error: solution load command failed (1)