%clear
The system cannot find the path specified.
cloudpickle >=0.5.0 : 1.2.1 (OK)
pygments >=2.0 : 2.4.2 (OK)
qtconsole >=4.5.5 : 4.5.5 (OK)
nbconvert >=4.0 : 5.5.0 (OK)
sphinx >=0.6.6 : 2.1.2 (OK)
pylint >=0.25 : 2.3.1 (OK)
psutil >=0.3 : 5.6.3 (OK)
qtawesome >=0.5.7 : 0.5.7 (OK)
qtpy >=1.5.0 : 1.8.0 (OK)
pickleshare >=0.4 : 0.7.5 (OK)
zmq >=17 : 18.0.0 (OK)
chardet >=2.0.0 : 3.0.4 (OK)
numpydoc >=0.6.0 : 0.9.1 (OK)
spyder_kernels >=1.5.0;<2.0.0: 1.5.0 (OK)
qdarkstyle >=2.7 : 2.7 (OK)
atomicwrites >=1.2.0 : 1.3.0 (OK)
diff_match_patch >=20181111 : 20181111 (OK)
watchdog : None (OK)
keyring : None (OK)
pexpect >=4.4.0 : 4.7.0 (OK)
pympler : None (OK)
sympy >=0.7.3 : 1.4 (OK)
cython >=0.21 : 0.29.12 (OK)
IPython >=4.0 : 7.6.1 (OK)
matplotlib >=2.0.0 : 3.1.0 (OK)
pandas >=0.13.1 : 0.24.2 (OK)
numpy >=1.7 : 1.16.4 (OK)
scipy >=0.17.0 : 1.2.1 (OK)
pyls >=0.28.2;<0.29.0 : 0.28.3 (OK)
rtree >=0.8.3 : 0.8.3 (OK)
This happens when your current working directory is a network mount. So avoid that until we fix it.
Same issue here with Spyder 3.3.6 as well. All other package versions being the same.
Things do work properly if the drive is mounted X:\Folder\To\Project but do not with just a network folder \\server.com\with\additional\Folder\To\Project\
This looks like a bug in IPython. We'll submit a pull request there to fix it.
Checking the issues of IPython seems like this is related to ipython/ipython#11488
Great work finding the issue there @dalthviz! Then, as I suspected, we need to submit a PR there to fix things here. Please do that.
Doing some testing, and after reading more carefully the issue in IPython (where the user specifies he is using Spyder 3.3.1), seems like the issue is actually in QtConsole and it's not only affecting the clear magic but also other magics like ls:

Testing with IPython the clear magic cls works as expected
Note: Probably we need to detect that a cd is being executed with an UNC path and change the actually command being executed to one using pushd (cmd doesn't support UNC paths by default). Using pushd mounts the UNC path to a drive.
Relevant code to check:
https://github.com/ipython/ipython/blob/a0c21526a456347f5f1f397dfb58bd0e7412e235/IPython/core/interactiveshell.py#L2468
Edit: The change needs to be implemented in ZMQInteractiveShell (ipykernel) or the InteractiveShell (IPython). The system_piped method needs to use AvoidUNCPath as is done in system_raw to handle UNC paths. Launching IPython from the cmd works without this since TerminalInteractiveShell uses system_raw as default handler for the system commands.
This is fixed in ipykernel 5.2.1. Conda packages should be available soon.