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In my .ssh directory I have the following files -

drwx------  2 rohit rohit 4096 Jun 22 03:34 ./
drwxr-xr-x 62 rohit rohit 4096 Jun 22 11:16 ../
-rw-r--r--  1 rohit rohit  402 May 25 15:19 authorized_keys
-rw-------  1 rohit rohit 1743 Oct 26  2011 id_rsa
-rw-r--r--  1 rohit rohit  402 Oct 26  2011 id_rsa.pub
-rw-r--r--  1 rohit rohit    0 Jun 22 03:34 known_hosts

On my another computer I have the following files -

drwx------  2 rohit  512 2012-06-22 11:10 .
drwxr-xr-x 41 rohit 1536 2012-06-22 11:34 ..
-rw-r--r--  1 rohit  402 2012-05-25 15:24 authorized_keys
-rw-------  1 rohit 1743 2012-05-30 13:02 id_rsa
-rw-------  1 rohit  630 2012-05-30 13:04 id_rsa.keystore
-rw-r--r--  1 rohit  797 2012-06-22 11:10 known_hosts

I know that id_rsa is my private key, id_rsa.pub is my public key, authorized keys are the public keys of the keys I have given access to and known hosts are the signatures of host I have connected to. What is the id_rsa.keystore file?

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Have you been working with any Java or JVM applications that make use of SSH or your public keys? .keystore, along with .jks, are the standard Java-keystore endings. They are usually managed using the keytool command

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The point of a keystore is to have all keys in one location protected with a single passphrase instead of being left all over the computer.

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