This enables portable SSH keys in cmder, enabling you to have full SSH access using cmder portably on a USB (for example). Please note that when you ssh-keygen, it will still default to %USERPROFILE%, so you will either have to change the path on generation, or manually move the keys to your %CMDER_ROOT%\config\.ssh directory.

user-profile.cmd

:: use this file to run your own startup commands
:: use  in front of the command to prevent printing the command

:: call "%GIT_INSTALL_ROOT%/cmd/start-ssh-agent.cmd"
:: set "PATH=%CMDER_ROOT%\vendor\whatever;%PATH%"


:: LS 2017-09-12_17.35.11
:: ======================
:: Copied from %CMDER_ROOT%\vendor\init.bat
:: Then changed line 61 following line from:

:: Find root dir
if not defined CMDER_ROOT (
    for /f "delims=" %%i in ("%ConEmuDir%\..\..") do set "CMDER_ROOT=%%~fi"
)

:: Remove trailing '\'
if "%CMDER_ROOT:~-1%" == "\" SET "CMDER_ROOT=%CMDER_ROOT:~0,-1%"


:: LS 2017-09-12_17.31.42
:: ======================
:: Copied in its entirety from %CMDER_ROOT%\vendor\git-for-windows\cmd\start-ssh-agent.cmd
:: Then changed line 61 following line from:
:: 
::     @SET "HOME=%USERPROFILE%"
:: 
:: to:
::     @SET "HOME=%CMDER_ROOT%\config"

@REM Do not use "echo off" to not affect any child calls.

@REM Enable extensions, the `verify` call is a trick from the setlocal help
@VERIFY other 2>nul
@SETLOCAL EnableDelayedExpansion
@IF ERRORLEVEL 1 (
    @ECHO Unable to enable extensions
    @GOTO failure
)

@REM Start the ssh-agent if needed by git
@FOR %%i IN ("git.exe") DO @SET GIT=%%~$PATH:i
@IF EXIST "%GIT%" @(
    @REM Get the ssh-agent executable
    @FOR %%i IN ("ssh-agent.exe") DO @SET SSH_AGENT=%%~$PATH:i
    @IF NOT EXIST "%SSH_AGENT%" @(
        @FOR %%s IN ("%GIT%") DO @SET GIT_DIR=%%~dps
        @FOR %%s IN ("!GIT_DIR!") DO @SET GIT_DIR=!GIT_DIR:~0,-1!
        @FOR %%s IN ("!GIT_DIR!") DO @SET GIT_ROOT=%%~dps
        @FOR %%s IN ("!GIT_ROOT!") DO @SET GIT_ROOT=!GIT_ROOT:~0,-1!
        @FOR /D %%s in ("!GIT_ROOT!\usr\bin\ssh-agent.exe") DO @SET SSH_AGENT=%%~s
        @IF NOT EXIST "!SSH_AGENT!" @GOTO ssh-agent-done
    )
    @REM Get the ssh-add executable
    @FOR %%s IN ("!SSH_AGENT!") DO @SET BIN_DIR=%%~dps
    @FOR %%s in ("!BIN_DIR!") DO @SET BIN_DIR=!BIN_DIR:~0,-1!
    @FOR /D %%s in ("!BIN_DIR!\ssh-add.exe") DO @SET SSH_ADD=%%~s
    @IF NOT EXIST "!SSH_ADD!" @GOTO ssh-agent-done
    @REM Check if the agent is running
    @FOR /f "tokens=1-2" %%a IN ('tasklist /fi "imagename eq ssh-agent.exe"') DO @(
        @ECHO %%b | @FINDSTR /r /c:"[0-9][0-9]*" > NUL
        @IF "!ERRORLEVEL!" == "0" @(
            @SET SSH_AGENT_PID=%%b
        ) else @(
            @REM Unset in the case a user kills the agent while a session is open
            @REM needed to remove the old files and prevent a false message
            @SET SSH_AGENT_PID=
        )
    )
    @REM Connect up the current ssh-agent
    @IF [!SSH_AGENT_PID!] == []  @(
        @ECHO Removing old ssh-agent sockets
        @FOR /d %%d IN (%TEMP%\ssh-??????*) DO @RMDIR /s /q %%d
    ) ELSE  @(
        @ECHO Found ssh-agent at !SSH_AGENT_PID!
        @FOR /d %%d IN (%TEMP%\ssh-??????*) DO @(
            @FOR %%f IN (%%d\agent.*) DO @(
                @SET SSH_AUTH_SOCK=%%f
                @SET SSH_AUTH_SOCK=!SSH_AUTH_SOCK:%TEMP%=/tmp!
                @SET SSH_AUTH_SOCK=!SSH_AUTH_SOCK:\=/!
            )
        )
        @IF NOT [!SSH_AUTH_SOCK!] == [] @(
            @ECHO Found ssh-agent socket at !SSH_AUTH_SOCK!
        ) ELSE (
            @ECHO Failed to find ssh-agent socket
            @SET SSH_AGENT_PID=
        )
    )
    @REM See if we have the key
    @SET "HOME=%CMDER_ROOT%\config"
    @"!SSH_ADD!" -l 1>NUL 2>NUL
    @SET result=!ERRORLEVEL!
    @IF NOT !result! == 0 @(
        @IF !result! == 2 @(
            @ECHO | @SET /p=Starting ssh-agent:
            @FOR /f "tokens=1-2 delims==;" %%a IN ('"!SSH_AGENT!"') DO @(
                @IF NOT [%%b] == [] @SET %%a=%%b
            )
            @ECHO. done
        )
        @"!SSH_ADD!"
        @ECHO.
    )
)

:ssh-agent-done
:failure

@ENDLOCAL & @SET "SSH_AUTH_SOCK=%SSH_AUTH_SOCK%" ^
          & @SET "SSH_AGENT_PID=%SSH_AGENT_PID%"

@ECHO %cmdcmdline% | @FINDSTR /l "\"\"" >NUL
@IF NOT ERRORLEVEL 1 @(
    @CALL cmd %*
)

Better yet. Add a symbolic link so that you don't need your ssh keys in two different places.

ln -s %USERPROFILE%\.ssh %CMDER_ROOT%\config\.ssh