Using the clear command doesn't clear the screen buffer.
This happens in both these situations:
Using "cls" command (while in DOS prompt) works fine.
Screenshot:

Hyper 1.3.3
Electron 1.4.16
win32 x64 10.0.15063
I ran into a similar issue on a similar system setup. This comment and this comment resolved the issue for me.
I had tried your suggestion and it worked (with both, cygwin and msys).
set TERM=cygwin
clear
I tried setting the Environment Variable so it would be fixed and every time I opened Hyper it would have it configured. It does not work, every time I open the console it has TERM=xterm-256color set, and I don't know where it's being set.

Update: I set a Windows environment variable, but I later found out that in hyper config file there's a key for environment variables.
I've tried looking in %USERPROFILE%\AppData\Local\lxss\home\%USER%.bashrc which is the location of the .bashrc file for "Bash on Ubuntu on Windows" without luck. any ideas? I think it would be best if Hyper added xterm-256color to the list of terms with such behavior though.
Mmmmm it's strange. It looks as if Hyper is the one setting the term to xterm-256color

I got it working from the Hyper configuration file:
env: {
TERM: 'cygwin'
}
I still think it's better to add xterm support to Hyper.
This is still an issue in version 1.4.3
I don't now the internals, but I don't know why this doesn't work, as it works fine in both CMD.exe and PowerShell.
Try updating to 1.4.7. It should be resolved now.
Still not working. Trying with the new 1.4.7 and with a clean .hyper.js config file.

I am on version 2.0.2 but still facing this issue. BTW I am on windows and 've set hyper for bash
I am on version 2.0.0 (stable) and still facing the issue where 'clear' does not work. The "shell" is set to shell: 'C:\\Program Files\\Git\\git-cmd.exe', and TERM is set to xterm-color. While setting TERM to cygwin allows 'clear' to work, it causes problems with vi/vim.
Same problem...
Temporary use CTRL + Shift + K to clear the commands!
hyper 2.1.1 stable
Windows, Git For Windows's Bash... Clear and \022[2J both fail to work properly in Hyper.
from Configuration
shell: 'C:\\Program Files\\Git\\bin\\bash.exe',
shellArgs: ['-i'],
env: {
CHERE_INVOKING: "1",
TERM: "cygwin",
},
Setting TERM in my ~/.profile to cygwin works, but the configuration option doesn't seem to be tacking for env.
@tiagoboeing - when I use CTRL + SHIFT + K it mostly clears, but the active line still has text clobbering the current line and as soon as ENTER is pressed the clobbered screen re-appears.
This problem is not only for Hyper, when you are using Git Bash for Windows and integrate in a terminal external, bugs happens.
I'm using Terminus and CTRL + SHIFT + K have same problem.
Most helpful comment
Same problem...
Temporary use
CTRL + Shift + Kto clear the commands!