keystore, pem, p12

You can extract a private key from a keystore with Java6 and OpenSSL. This all depends on the fact that both Java and OpenSSL support PKCS#12-formatted keystores. To do the extraction, you first usekeytool to convert to the standard format. Make sure you use the same password for both files (private key password, not the keystore password) or you will get odd failures later on in the second step.

keytool -importkeystore -srckeystore keystore.jks \
    -destkeystore intermediate.p12 -deststoretype PKCS12

Next, use OpenSSL to do the extraction to PEM:

openssl pkcs12 -in intermediate.p12 -out extracted.pem -nodes

You should be able to handle that PEM file easily enough; it's plain text with an encoded unencrypted private key and certificate(s) inside it (in a pretty obvious format).

export private key:

keytool.exe -importkeystore -srcstoretype JKS -srckeystore my-release-key.keystore -deststoretype PKCS12 -destkeystore keys.pk12.der
openssl.exe pkcs12 -in keys.pk12.der -nodes -out private.rsa.pem

edit private.rsa.pem and leave "-----BEGIN PRIVATE KEY-----" to "-----END PRIVATE KEY-----" paragraph, then:

openssl.exe base64 -d -in private.rsa.pem -out private.rsa.der

export public key:

keytool.exe -exportcert -keystore my-release-key.keystore -storepass <KEYSTORE_PASSWORD> -alias alias_name -file public.x509.der

sign apk:

java -jar SignApk.jar public.x509.der private.rsa.der input.apk output.apk