Git Integration for Jira Self-Managed (Data Center/Server) Documentation

How to disable “Discard cloned files” feature (Windows/Linux)

The Remove Discard files feature is deprecated and the purpose of this article is to guide you on how to completely disable this setting while preserving all integration settings such as project mapping, users’ PATS and other integration settings.

This guide applies to Jira instance with GIJ v4.11 and below.

1. Update Git Integration for Jira

Upgrade to the latest version of Git Integration for Jira supporting the Discard cloned files feature (GIJ v4.16 as of now).

Go to the Manage apps page and expand Git Integration for Jira under Installed apps.

GIJ under Installed apps showing Update button highlighted

Click Update to upgrade the Git Integration for Jira app to the newest version.

2. Verify that a Git client is installed

Make sure that a Git client is installed on the machine where the Jira instance is running.. Use the following command to check the installed Git version:

git --version

3. On Windows, verify installed Powershell version (skip this step for Linux)

Ensure that PowerShell version 5.x or higher is installed on the machine where the Jira instance is running.

Shows the PowerShell version command example in the Command prompt window

4. Disable webhooks on “Webhooks” page

On the Manage repositories page, click Webhooks on the sidebar then click Disabled.

Shows how to access the Webhooks page via Git menu then Manage repositories then on the sidebar click on Webhooks tab then click on Disabled radio button

5. Take note of the following General settings

Make sure to write down the following settings and save it for use later:

Repository indexing interval
Garbage collection and Revision validation interval
Git roll up issue tab
Git commits issue and project tabs

Then, set the scheduled job frequency to a large value. For example:

Repository indexing interval = 100000
Garbage collection and Revision validation interval = 100000

Also, disable the following settings to make GIJ repositories temporarily unavailable:

Set Git roll up issue tab to Do not display
Set Git commits issue and project tabs to Do not display
Untick the Enable repository browser setting
Untick the Show Git Integration panel on issue pages setting
Untick the Enable Automation for Jira (A4J) triggers setting
Untick the Enable JQL searching using commit information setting

6. Disable all repositories/integrations via Actions

Click the Disable all button on the Manage repositories page.

Shows Manage repositories page while highlighting the "Disable all" button

7. Clear the indexing queue

On your Jira dashboard Git menu, click Indexing queue.

Click on the Clear queue button to clear the indexing queue.

8a. Powershell script for Windows

#requires -version 5
[CmdletBinding()]
param (
    [Parameter(Mandatory=$false,Position=0)]
    [string]$FullRun
)

$ErrorActionPreference = 'Stop'

$ScriptDirectory = Split-Path -Path $PSScriptRoot -Leaf
if ( $ScriptDirectory -ne "git-plugin" ) {
    Write-Output "The script should be run in jira/home/data/git-plugin directory! Current directory is `"$PSScriptRoot`"."
    return
}

function Remove-Tree()
{
    [CmdletBinding()]
    param(
        [Parameter(Mandatory=$true)]
        [string]$Path
    )

    if ( Test-Path -LiteralPath $Path -PathType Container ) {
        @(Get-ChildItem -LiteralPath $Path -Directory -Force).ForEach({ Remove-Tree -Path $_.FullName })
        @(Get-ChildItem -LiteralPath $Path -File -Force).ForEach({ Remove-Item -LiteralPath $_.FullName -Force })
    }
    Remove-Item -LiteralPath $Path -Force
}

function Clear-GitRepo()
{
    [CmdletBinding()]
    param(
        [Parameter(Mandatory=$true)]
        [string]$GitRepoFolder
    )

    Set-Location -LiteralPath $GitRepoFolder
    Write-Output ""

    if ( -not (Test-Path -LiteralPath 'config' -PathType Any) ) {
        Write-Output "skip $GitRepoFolder folder. It doesn't contain config."
        Set-Location -Path ".."
        return
    }

    Write-Output "delete files from $GitRepoFolder except 4 files: config, HEAD, repo.auto.json, repo.auto.json.gitforjira.lock"

    @(Get-ChildItem -Force | Where-Object {$_.Name -notin "config", "HEAD", "repo.auto.json", "repo.auto.json.gitforjira.lock"}).ForEach({
        Remove-Tree -Path $_.FullName
    })

    $isHeadExists = Test-Path -LiteralPath 'HEAD' -PathType Any
    if ( $isHeadExists ) {
        Write-Output "move 'HEAD' to 'HEAD-gij-backup' file"
        Move-Item -Path 'HEAD' -Destination 'HEAD-gij-backup' -Force
    }

    Write-Output "init a bare repository with the same config"
    $DummyDir = 'non-existent-git-template-directory'
    try {
        git init --bare --template=$DummyDir --quiet
    }
    catch [System.Management.Automation.RemoteException] {
        if ( -not ($_.Exception -like "*$DummyDir*") ) {
            throw
        }
    }

    if ( $isHeadExists ) {
        Write-Output "restore 'HEAD' file"
        Move-Item -Path 'HEAD-gij-backup' -Destination 'HEAD' -Force
    }

    Set-Location -Path ".."
}

function Test-RunType()
{
    [CmdletBinding()]
    param(
        [Parameter(Mandatory=$true)]
        [string]$GitRepoFolder,

        [Parameter(Mandatory=$true)]
        [boolean]$IsFullRun
    )

    if( $IsFullRun ) {
        Clear-GitRepo -GitRepoFolder $GitRepoFolder
    } else {
        Write-Output (Split-Path -Path $GitRepoFolder -Leaf)
    }
}

git --version
Write-Output ""

$IsFullRunSet = $PSBoundParameters.Count -ge 1
if ( $IsFullRunSet ) {
    Write-Output "Processing of Git repositories has been started. It may take several minutes so please be patient."
}
@(Get-ChildItem -Path "." -Directory -Force -Exclude "scripts","weblinking").ForEach({
    Test-RunType -GitRepoFolder $_ -IsFullRun $IsFullRunSet
})

Save this script to clearDataInRepositories.ps1.

8b. ShellScript for Linux

#!/bin/bash
set -eo pipefail

clearGitRepo(){
    cd "${1}"
    echo ""

    if [[ ! -f "config" ]]; then
        echo "skip ${1} folder. It doesn't contain config."
        cd ..
        return 0
    fi

    echo "delete files from ${1} except 4 files: config, HEAD, repo.auto.json, repo.auto.json.gitforjira.lock"

    find . -maxdepth 1 ! -name 'config' ! -name 'HEAD' ! -name 'repo.auto.json' ! -name 'repo.auto.json.gitforjira.lock' ! -name '.' ! -name '..' -exec rm --force --recursive {} ;

    IS_HEAD_EXISTS=true
    if [[ ! -f "HEAD" ]]; then
        IS_HEAD_EXISTS=false
    fi

    if $IS_HEAD_EXISTS; then
        echo "move 'HEAD' to 'HEAD-gij-backup' file"
        mv --force HEAD HEAD-gij-backup
    fi

    dummyDir=non-existent-git-template-directory
    echo "init a bare repository with the same config. Ignore the next warning if it says about '${dummyDir}'."
    git init --bare --template=${dummyDir} --quiet

    if $IS_HEAD_EXISTS; then
        echo "restore 'HEAD' file"
        mv --force HEAD-gij-backup HEAD
    fi

    cd ..
}
export -f clearGitRepo

dryOrNot(){
    if [ -z "${1}" ]; then
        cat <&0
    else
        xargs --max-args=1 --delimiter='n' bash -c 'clearGitRepo "${0}"'
    fi
}
export -f dryOrNot

SCRIPT_DIRECTORY=$(basename $PWD)
if [ "${SCRIPT_DIRECTORY}" != "git-plugin" ]; then
    echo "The script should be run in jira/home/data/git-plugin directory! Current directory is '$SCRIPT_DIRECTORY'."
    exit 1
fi

git --version
echo ""

ls --directory */ | grep --invert-match --word-regexp --extended-regexp 'scripts/|weblinking/' | dryOrNot "${1}"

Save this script to clearDataInRepositories.sh.

9. Review repository folders that will be cleared

Run the script without arguments in jira/home/data/git-plugin folder to preview which repository folders are going to be cleared.

On Windows (in PowerShell console):
.clearDataInRepositories.ps1

On Linux (Terminal):
./clearDataInRepositories.sh

Important!
For mounted shared folders on the same server as Jira, you will need to unmount them first before proceeding to step 10.

Note
If your Jira self-managed instance and Git repositories are on the same server – the git repositories are not affected since the script execution in step 10 will only process the folder where the cloned repositories reside (jira/home/data/git-plugin). It is dangerous if any of the folders is not a clone created by the GIJ plugin (i.e. if it’s the origin Git repository and it does not have other full clones).

10. Clear the repository clone folders

The script loops through all the folders in jira/home/data/git-plugin (where the cloned repositories reside). For each folder, the contents are deleted such as git files structure (except several config files) and initializes a bare Git repository using the same configuration.

Execute the script with one argument in jira/home/data/git-plugin folder on behalf of the Jira user (read here):

On Windows (in PowerShell console):
.clearDataInRepositories.ps1 go

On Linux (Terminal):
./clearDataInRepositories.sh go

11. Disable the Remove Discard files setting

Go to General settings (Jira dashboard menu Git ➜ Manage repositories ➜ General settings [left sidebar]).
Scroll down to the Advanced settings and click to expand the hidden options.
For the Discard cloned files in Jira home directory setting, set it to Keep all cloned files. No storage savings. All features available.

12. Enable all the repositories/integrations back

On the Manage repositories page, click the Enable all to reconnect all integration repositories to Git Integration for Jira.

Shows the Manage repositories page highlighting the Enable all button

If you only plan to enable specific repositories, use the checkboxes at the Enabled column of the repositories list.

13. Perform a Reset all of the indexes

On the Manage repositories page, click on Indexing ➜ Reset all indexes.

Shows where to access this function -- Manage repositories page then click on Indexing drop down then click "Reset all indexes"

14. Revert back the Generals settings

Change back the following settings to the saved values from step 5:

Repository indexing interval
Garbage collection and Revision validation interval
Git roll up issue tab
Set Git commits issue and project tabs

Also, enable the following settings to make GIJ repositories available again:

Tick on the Enable repository browser setting
Tick on the Show Git Integration panel on issue pages setting
Tick on the Enable Automation for Jira (A4J) triggers setting
Tick on the Enable JQL searching using commit information setting

15. Enable back webhooks

On the Manage repositories page, click Webhooks on the sidebar then click Enabled.

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