Here's a PowerShell function which does the equivalent of update-database in the Package Manager console, from a normal PowerShell window, using EF x.x.x. 
I'm using it from the command line as part of a 'full build' process on my dev machine;
function Update-Database($solutionDir, $projectBinDir, $assemblyName, $appConfigFile)
{
    $efMigrateExe = "$solutionDir\packages\EntityFramework.*\tools\migrate.exe"
    Write-Host "Updating Entity Framework Database"
    Write-Host "    Migrate.exe at $efMigrateExe"
    Write-Host "    EF project binary at $projectBinDir"
    Write-Host "    EF config at $appConfigFile"
    . "$efMigrateExe" "$assemblyName" /startupConfigurationFile="$appConfigFile" /startupDirectory="$projectBinDir"
}
The parameters are;
$solutionDir -- the directory where your solution lives; the parent of the packages folder.
$projectBinDir -- the <something>\bin\debug directory containing the assembly with your DbContext.
$assemblyName -- the name of the assembly file, like MyEfProject.dll
appConfigFile -- the name of the app.config or web.config file which contains connection strings etc. Equivalent to using -StartupProjectName in the Package Manager console.