Git SSH Connection Issues in IntelliJ IDEA: RSA Public Key Padding Errors and known_hosts Hashing Solutions

Problem Background and Error Analysis

In IntelliJ IDEA development environments, SSH connection issues with Git version control represent a common technical challenge. Users report encountering fatal: Could not read from remote repository errors when executing git fetch or git push operations, accompanied by specific exception stack traces: java.io.IOException: Padding in RSA public key!. This error indicates that the SSH client encountered data structure issues when processing RSA public keys, specifically within the com.trilead.ssh2.signature.RSASHA1Verify.decodeSSHRSAPublicKey method.

Technical Principles Deep Dive

The SSH protocol utilizes known_hosts files to store verified remote host keys, preventing man-in-the-middle attacks. IntelliJ IDEA's built-in SSH client implementation, based on the Trilead SSH2 library, handles known_hosts files differently from standard OpenSSH clients. The key distinction lies in the requirement for host entries to be stored in hashed format within the built-in client, whereas standard OpenSSH clients default to plaintext hostnames.

Hashing processing converts hostnames into fixed-length strings using SHA-1 hash algorithms, enhancing security but potentially causing compatibility issues. When known_hosts files contain mixed hashed and non-hashed entries, IntelliJ's built-in SSH client fails to properly parse the file content, resulting in RSA public key decoding failures.

Problem Reproduction and Diagnostic Methods

The described problem scenario demonstrates typical characteristics: Git operations fail through IntelliJ IDEA's graphical interface but succeed when manually executing identical Git commands in the built-in terminal. This discrepancy clearly points to compatibility issues between IDE-built components and system-native tools.

Diagnostic procedures should include:

1. Examining ~/.ssh/known_hosts file format for mixed-format entries
2. Verifying SSH key permissions, ensuring private key files have 600 permissions
3. Using ssh -vvv git@server command for detailed connection debugging
4. Comparing version differences between built-in and native SSH clients

Core Solution Implementation

Based on problem analysis, two effective solutions are provided:

Solution 1: known_hosts File Reconstruction

Completely remove the existing known_hosts file, allowing IntelliJ IDEA to recreate a purely hashed format file. Specific operational steps:

# Backup existing known_hosts file
cp ~/.ssh/known_hosts ~/.ssh/known_hosts.backup

# Remove original file
rm ~/.ssh/known_hosts

# Execute Git operations through IntelliJ to automatically create new hashed known_hosts file

Note that this approach requires all SSH clients to support hashed known_hosts format. Other SSH clients accessing the same hosts need corresponding configuration adjustments.

Solution 2: Switch to Native SSH Client

In IntelliJ IDEA settings, change the SSH executable from built-in to native:

Settings → Version Control → Git → SSH executable: Native

This solution leverages the system's native SSH client, avoiding known_hosts format compatibility issues while benefiting from system-level SSH configuration and updates.

Extended Technical Considerations

Referencing SSH key permission issues mentioned in supplementary materials, ensure:

• SSH private key file permissions set to 600: chmod 600 ~/.ssh/id_rsa
• Public key correctly added to Git server account
• SSH connection uses correct username and host address

For Windows system users, also be aware of potentially cached old credentials in Credential Manager, which can be cleaned through the control panel's credential manager.

Prevention and Best Practices

To prevent recurrence of similar issues, recommend:

• Unifying known_hosts file handling strategies across all SSH clients
• Regularly updating IntelliJ IDEA and system SSH client versions
• Establishing standardized troubleshooting procedures for SSH connection issues
• Implementing unified SSH configuration standards in team development environments

Through systematic problem analysis and solution implementation, developers can effectively resolve various technical obstacles in Git SSH connections within IntelliJ IDEA, ensuring smooth version control workflow operation.