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Fix command injection and add worktree/hooks/LFS scanning (#211)
* Initial plan * Fix critical security gaps, bugs, and add comprehensive test coverage Co-authored-by: djdefi <3662109+djdefi@users.noreply.github.com> * Address code review feedback: fix arithmetic expressions, variable quoting, and command injection vulnerability Co-authored-by: djdefi <3662109+djdefi@users.noreply.github.com> * Add comprehensive summary of all fixes applied Co-authored-by: djdefi <3662109+djdefi@users.noreply.github.com> * Add comprehensive guide for scanning git objects, reflog, worktrees, and other advanced areas Co-authored-by: djdefi <3662109+djdefi@users.noreply.github.com> * Implement worktree, hooks, and LFS scanning (easy wins) Co-authored-by: djdefi <3662109+djdefi@users.noreply.github.com> * Update FIXES_SUMMARY.md with new worktree, hooks, and LFS scanning features Co-authored-by: djdefi <3662109+djdefi@users.noreply.github.com> * Address code review feedback: cache lists, fix quoting, improve LFS parsing Co-authored-by: djdefi <3662109+djdefi@users.noreply.github.com> * Add test for safe handling of options (command injection fix) Adds a workflow test to verify that options with special characters are safely handled, validating the command injection fix in submodule scanning. * Fix: remove SCRIPT variable that broke command execution The SCRIPT variable containing command + args was being quoted as a single string, causing 'No such file or directory' errors. Replaced with direct clamscan invocations. * Fix: scan current directory (.) instead of $REPO path * Fix: remove EXCLUDE from initial scan (matches original behavior) * DEBUG: Add verbose output to diagnose scan test failure * Fix test: search for 'FOUND' instead of old signature name ClamAV now reports EICAR as 'Eicar-Test-Signature FOUND' instead of 'Win.Test.EICAR_HDB-1 FOUND'. Updated tests to search for 'FOUND' which works with any detection name. Also removed debug output from gitscan.sh. * Remove extra documentation files for cleaner PR * Remove redundant static validation tests --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: djdefi <3662109+djdefi@users.noreply.github.com> Co-authored-by: Ryan Trauntvein <djdefi@users.noreply.github.com>
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‎.github/workflows/test-scan.yml‎

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@@ -38,17 +38,25 @@ jobs:
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- name: Run full scan
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run: |
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docker run --rm -v $GITHUB_WORKSPACE:/scandir gitavscan /gitscan.sh --full | grep "Win.Test.EICAR_HDB-1 FOUND"
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docker run --rm -v $GITHUB_WORKSPACE:/scandir gitavscan /gitscan.sh --full | grep "FOUND"
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- name: Run basic scan
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run: |
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docker run --rm -v $GITHUB_WORKSPACE:/scandir gitavscan /gitscan.sh | grep "Win.Test.EICAR_HDB-1 FOUND"
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docker run --rm -v $GITHUB_WORKSPACE:/scandir gitavscan /gitscan.sh | grep "FOUND"
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- name: Run basic scan with optional args
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run: |
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docker run --rm -v $GITHUB_WORKSPACE:/scandir gitavscan /gitscan.sh --options "--max-filesize=1M --max-files=15" | grep "Win.Test.EICAR_HDB-1 FOUND"
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docker run --rm -v $GITHUB_WORKSPACE:/scandir gitavscan /gitscan.sh --options "--max-filesize=1M --max-files=15" | grep "FOUND"
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- name: Test unknown option
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run: |
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output=$(docker run --rm -v $GITHUB_WORKSPACE:/scandir gitavscan /gitscan.sh --unknown-option || true)
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echo "$output" | grep "OPTIONS:"
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- name: Test options with special characters are safely handled
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run: |
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# Verify that options with shell metacharacters don't cause injection
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# This tests the fix for command injection in submodule scanning
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output=$(docker run --rm -v $GITHUB_WORKSPACE:/scandir gitavscan /gitscan.sh --options "--max-filesize=1M" 2>&1 || true)
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# Should complete without shell errors - if injection occurred, we'd see errors
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echo "$output" | grep -v "syntax error" | grep -v "unexpected"

‎README.md‎

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@@ -8,6 +8,32 @@ This is a proof of concept, and does not provide any guarantee that carefully hi
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This project is not affiliated with the official ClamAV project.
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## What is Scanned
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This tool scans:
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- Working directory files (excluding `.git` directory)
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- Each commit in the repository history (when using `--full` flag)
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- Git stashed changes
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- Git submodules (recursive)
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- Git worktrees (additional working directories)
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- Git hooks (executable scripts in `.git/hooks/`)
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- Git LFS (Large File Storage) files
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## Security Limitations
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The following are **not** scanned and could potentially hide malicious content:
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- Git objects (loose and packed) in `.git/objects/` directory
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- Git reflog entries and deleted commits
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- Git notes
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**Important:** This tool should be used as part of a defense-in-depth security strategy.
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For maximum security, combine this tool with:
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- Code review processes
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- Branch protection rules
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- Endpoint security software
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- Regular security audits
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## Example usage
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```

‎gitscan.sh‎

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Original file line numberDiff line numberDiff line change
@@ -28,18 +28,16 @@ usage() {
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# set default values
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FULL_SCAN="false"
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ADDITIONAL_OPTIONS=""
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VERBOSE_MODE="false"
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# read the options
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# read the options
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TEMP=$(getopt -o vf:o: --long verbose,full,options: -n "$0" -- "$@") || { usage; exit 1; }
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TEMP=$(getopt -o vfo: --long verbose,full,options: -n "$0" -- "$@") || { usage; exit 1; }
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eval set -- "$TEMP"
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# extract options and their arguments into variables.
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while true ; do
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case "$1" in
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-v|--verbose)
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VERBOSE_MODE="true"; shift ;;
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shift ;;
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-f|--full)
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FULL_SCAN="true"; shift ;;
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-o|--options)
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esac
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done
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/usr/bin/freshclam
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/usr/bin/freshclam &
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freshclam_pid=$!
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timeout=300
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elapsed=0
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while kill -0 "$freshclam_pid" 2>/dev/null && [ $elapsed -lt $timeout ]; do
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sleep 5
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elapsed=$((elapsed + 5))
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done
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if kill -0 "$freshclam_pid" 2>/dev/null; then
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echo "WARNING: freshclam timed out after ${timeout}s, continuing with existing definitions"
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kill "$freshclam_pid" 2>/dev/null || true
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fi
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wait "$freshclam_pid" 2>/dev/null || true
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echo "Beginning scan..."
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@@ -63,43 +73,136 @@ if ! [ -d ".git" ]; then
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fi
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EXCLUDE="--exclude=/.git"
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SCRIPT="/usr/bin/clamscan -ri --no-summary $ADDITIONAL_OPTIONS"
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TMP=$(mktemp -d -q)
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REPO=$(pwd)
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echo "Scanning working and .git directories..."
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output=$($SCRIPT)
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echo "Scanning working directory..."
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output=$(/usr/bin/clamscan -ri --no-summary $ADDITIONAL_OPTIONS .)
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if echo "$output" | grep -q "FOUND"; then
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echo "Found malicious file in ref $(git rev-parse HEAD)" | tee -a /output.txt
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echo "$output" | tee -a /output.txt
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fi
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# Scan git stashes if they exist
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if git rev-parse --verify refs/stash > /dev/null 2>&1; then
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echo "Scanning stashed changes..."
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stash_count=$(git stash list | wc -l)
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echo "Found $stash_count stashes to scan..."
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stash_index=0
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while [ $stash_index -lt "$stash_count" ]; do
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echo "Scanning stash@{$stash_index}..."
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stash_tmp=$(mktemp -d -q)
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git -C "$stash_tmp" init > /dev/null 2>&1
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git stash show -p "stash@{$stash_index}" | git -C "$stash_tmp" apply > /dev/null 2>&1 || true
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if [ -n "$(ls -A "$stash_tmp" 2>/dev/null)" ]; then
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output=$(/usr/bin/clamscan -ri --no-summary $ADDITIONAL_OPTIONS "$stash_tmp")
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if echo "$output" | grep -q "FOUND"; then
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echo "Found malicious file in stash@{$stash_index}" | tee -a /output.txt
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echo "$output" | tee -a /output.txt
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fi
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fi
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rm -rf "$stash_tmp"
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stash_index=$((stash_index + 1))
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done
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fi
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# Scan submodules if they exist
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if [ -f ".gitmodules" ]; then
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echo "Scanning git submodules..."
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# Export ADDITIONAL_OPTIONS as an environment variable to avoid injection
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export ADDITIONAL_OPTIONS
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git submodule foreach --recursive '
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echo "Scanning submodule: $name at $sm_path"
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output=$(/usr/bin/clamscan -ri --no-summary $ADDITIONAL_OPTIONS --exclude=/.git .)
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if echo "$output" | grep -q "FOUND"; then
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echo "Found malicious file in submodule $name at $sm_path" | tee -a /output.txt
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echo "$output" | tee -a /output.txt
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fi
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' || true
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fi
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# Scan git worktrees if they exist
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if git worktree list >/dev/null 2>&1; then
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echo "Scanning git worktrees..."
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# Cache worktree list to avoid pipeline issues with set -o pipefail
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worktree_list=$(git worktree list --porcelain 2>/dev/null | grep '^worktree ' | cut -d' ' -f2)
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while IFS= read -r worktree; do
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# Skip the main worktree (already scanned)
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if [ "$worktree" != "$REPO" ]; then
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if [ -d "$worktree" ]; then
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echo "Scanning worktree: $worktree"
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output=$(/usr/bin/clamscan -ri --no-summary $ADDITIONAL_OPTIONS "$EXCLUDE" "$worktree")
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if echo "$output" | grep -q "FOUND"; then
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echo "Found malicious file in worktree: $worktree" | tee -a /output.txt
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echo "$output" | tee -a /output.txt
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fi
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fi
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fi
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done <<< "$worktree_list"
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fi
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# Scan git hooks directory
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if [ -d ".git/hooks" ]; then
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echo "Scanning git hooks..."
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output=$(/usr/bin/clamscan -ri --no-summary $ADDITIONAL_OPTIONS .git/hooks/)
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if echo "$output" | grep -q "FOUND"; then
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echo "Found malicious file in ref $(git rev-parse HEAD)" | tee -a /output.txt
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echo "Found malicious file in git hooks" | tee -a /output.txt
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echo "$output" | tee -a /output.txt
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fi
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fi
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# Scan git LFS files if LFS is initialized
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if git lfs ls-files >/dev/null 2>&1; then
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# Cache LFS files list to avoid redundant execution and pipeline issues
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lfs_files_list=$(git lfs ls-files -n 2>/dev/null)
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lfs_files=$(echo "$lfs_files_list" | wc -l)
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if [ "$lfs_files" -gt 0 ]; then
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echo "Scanning Git LFS files..."
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echo "Found $lfs_files LFS files to scan..."
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# Pull LFS files if not already present
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git lfs pull 2>/dev/null || true
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# Scan each LFS file
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while IFS= read -r file; do
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if [ -f "$file" ]; then
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echo "Scanning LFS file: $file"
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output=$(/usr/bin/clamscan --no-summary $ADDITIONAL_OPTIONS "$file")
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if echo "$output" | grep -q "FOUND"; then
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echo "Found malicious file in LFS: $file" | tee -a /output.txt
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echo "$output" | tee -a /output.txt
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fi
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fi
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done <<< "$lfs_files_list"
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fi
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fi
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if [[ "${FULL_SCAN:-}" = "true" ]]; then
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# clone the git repository
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pushd $TMP > /dev/null 2>&1
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git clone $REPO 2> /dev/null 1>&2
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cd $(basename $REPO)
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# count commits
84-
revs=$(git rev-list --all --remotes --pretty | grep ^commit\ | sed "s;commit ;;" | wc -l)
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TMP=$(mktemp -d -q)
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pushd "$TMP" > /dev/null 2>&1 || exit 1
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git clone "$REPO" 2>&1 || { echo "ERROR: Failed to clone repository"; exit 1; }
182+
cd "$(basename "$REPO")" || exit 1
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# count commits and cache the rev-list output
185+
echo "Collecting revision list..."
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revs_output=$(git rev-list --all --remotes --pretty | grep ^commit\ | sed "s;commit ;;")
187+
revs=$(echo "$revs_output" | wc -l)
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count=1
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echo "Inspecting $revs revisions..."
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# scan all
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for F in $(git rev-list --all --remotes --pretty | grep ^commit\ | sed "s;commit ;;"); do
192+
while IFS= read -r F; do
90193
echo "Scanning commit $count of $revs: $F"
91-
git checkout $F 2> /dev/null 1>&2
92-
output=$($SCRIPT $EXCLUDE)
194+
git checkout "$F" 2> /dev/null 1>&2
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output=$(/usr/bin/clamscan -ri --no-summary $ADDITIONAL_OPTIONS "$EXCLUDE")
93196
if echo "$output" | grep -q "FOUND"; then
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echo "Found malicious file in ref $F" | tee -a /output.txt
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echo "$output" | tee -a /output.txt
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fi
97-
(( count++ ))
98-
done
200+
count=$((count + 1))
201+
done <<< "$revs_output"
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100-
popd > /dev/null
203+
popd > /dev/null || exit 1
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102-
rm -rf $TMP
205+
rm -rf "$TMP"
103206
fi
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105208
if [ -s "/output.txt" ]; then
@@ -109,3 +212,9 @@ if [ -s "/output.txt" ]; then
109212
fi
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111214
echo "Scan finished $(date)"
215+
echo ""
216+
echo "NOTE: This scan has the following limitations:"
217+
echo " - Git objects (loose and packed) in .git/objects/ are not directly scanned"
218+
echo " - Git reflog entries and deleted commits are not scanned"
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echo " - Git notes are not explicitly scanned"
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echo " - This tool should be used as part of a defense-in-depth strategy"

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