Segmentation fault issues with `lg2`

[saiki-k]

I am currently using lg2 to sync a git repository using a custom shell script, that I run using an iOS shortcut.

Here's the shortcut for a general idea.

The issue with this shortcut though, lg2 status often errors out with segmentation faults. I observed that if I manually open and exit a-Shell from the iOS app switcher, these segfaults go away -- actually, the exit bookend commands that you see in the above shortcut screenshot were added later, to simulate this behaviour.

However, I have noticed that exits don't destroy the instance. When I open the app after running an exit, I am often times presented with an old instance. Added a short recording below that demonstrates this issue.

a-Shell.exit.issue.mp4

I am positive that if I can somehow program the proper "close everything" behaviour into the shortcut, I don't have to keep wrangling with the whole "open and close a-Shell before running the shortcut" act. I am presuming the segmentation faults have something to do with the shortcut creating a new session and not properly GC-ing the whole thing.

Any pointers on how to manage this better, if it can be managed in the first place, or a workaround if I am plainly missing something... are welcome and appreciated.

[holzschu]

One key element is that exit does not actually end the app on an iPhone (it's an OS/Apple limitation). It closes the current window on an iPad (which is the same as ending the app if there is only one window open).

The current TestFlight version has multiple fixes for lg2; you could check if it fixed your issues: https://testflight.apple.com/join/WUdKe3f4

Finally, it's much easier for me to fix an issue if I can reproduce it on my end (I have access to a debugger, which tells me exactly which variable wasn't properly released). That's what allowed me to fix quickly #971 and #972.

[saiki-k]

Thank you so much for looking into this. I'll indeed checkout the TestFlight version, and post an update here.

Additionally, I've also added the lg2_sync.sh file (in a new comment) below for your reference.

If the TestFlight version still has issues, I shall look into setting up a repo that you can potentially use to reproduce and debug the/any issue(s).

---

More on exit

You mentioned that exit doesn't close the app, I understand this, and I want to highlight that this was not my original intent.

As you can see in the video I have uploaded above... exit is failing to close the existent window on an iPhone.

I see that you say:

It closes the current window on an iPad (which is the same as ending the app if there is only one window open).

...is this not what happens on an iPhone?

[saiki-k]

Following are the contents of the lg2_sync.sh script. It can be put inside a(ny) git repo two folders down the root (say ./meta/scripts, considering . is the root of the repo), and can be run from there, to sync the contents of the repo with the corresponding remote (already set for the repo).

#!/bin/sh
# Git sync script for Obsidian vault on a-Shell (iOS)
# Uses lg2 (libgit2) instead of git

GIT_CONFIG_USER_NAME="<YOUR_GIT_USER_NAME>"
GIT_CONFIG_USER_EMAIL="<YOUR_GIT_EMAIL>"

RED='\033[0;31m'
GREEN='\033[0;32m'
YELLOW='\033[1;33m'
NO_COLOR='\033[0m'

print_msg() {
    printf "%b\n" "$1"
}

ORIGINAL_DIR=$(pwd)

SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
VAULT_DIR="$(cd "$SCRIPT_DIR/../.." && pwd)"
VAULT_NAME="$(basename "$VAULT_DIR")"

print_msg "${YELLOW}Starting git sync for the vault \"${VAULT_NAME}\" on a-Shell...${NO_COLOR}"

cd "$VAULT_DIR" || {
    print_msg "${RED}Error: Could not navigate to vault directory${NO_COLOR}"
    exit 1
}

if [ ! -d ".git" ]; then
    print_msg "${RED}Error: Not a git repository${NO_COLOR}"
    cd "$ORIGINAL_DIR"
    exit 1
fi

# Check if any SSH key exists
SSH_KEY_PATH=""
for key_type in id_ed25519 id_rsa id_ecdsa id_dsa; do
    if [ -f "$HOME/Documents/.ssh/${key_type}.pub" ]; then
        SSH_KEY_PATH="$HOME/Documents/.ssh/${key_type}"
        break
    fi
done

if [ -z "$SSH_KEY_PATH" ]; then
    print_msg "${RED}Error: No SSH keypair found in $HOME/Documents/.ssh/${NO_COLOR}"
    print_msg "${YELLOW}Please generate an SSH key pair first:${NO_COLOR}"
    print_msg "  ssh-keygen -t ed25519 -C \"$GIT_CONFIG_USER_EMAIL\""
    cd "$ORIGINAL_DIR"
    exit 1
fi

# Configure lg2 if not already set
if [ -z "$(lg2 config user.name 2>/dev/null)" ]; then
    lg2 config user.name "$GIT_CONFIG_USER_NAME" 2>/dev/null || true
fi

if [ -z "$(lg2 config user.email 2>/dev/null)" ]; then
    lg2 config user.email "$GIT_CONFIG_USER_EMAIL" 2>/dev/null || true
fi

if [ -z "$(lg2 config user.identityFile 2>/dev/null)" ]; then
    lg2 config user.identityFile "$SSH_KEY_PATH" 2>/dev/null || true

    lg2 config user.password "" 2>/dev/null || true
    print_msg "${YELLOW}Note: user.password set to empty. Change it if your SSH key has a passphrase.${NO_COLOR}"
fi

get_timestamp() {
    date +"%Y.%m.%d %H:%M:%S"
}

HOSTNAME="a-Shell on iOS"
TIMESTAMP=$(get_timestamp)
COMMIT_MSG="Update vault from ${HOSTNAME} (${TIMESTAMP})"

print_msg "${YELLOW}Checking status...${NO_COLOR}"

if [ -z "$(lg2 status --porcelain)" ]; then
    print_msg "${GREEN}No local changes to commit${NO_COLOR}"
else
    print_msg "${YELLOW}Local changes detected, staging files...${NO_COLOR}"
    lg2 add .
    
    print_msg "${YELLOW}Committing changes...${NO_COLOR}"
    if ! lg2 commit -m "$COMMIT_MSG"; then
        print_msg "${RED}Error: Commit failed${NO_COLOR}"
        cd "$ORIGINAL_DIR"
        exit 1
    fi
    print_msg "${GREEN}Changes committed successfully${NO_COLOR}"
fi

if ! lg2 remote show origin --verbose >/dev/null 2>&1; then
    print_msg "${RED}Error: No remote 'origin' configured${NO_COLOR}"
    cd "$ORIGINAL_DIR"
    exit 1
fi

print_msg "${YELLOW}Pulling changes from remote...${NO_COLOR}"

# When local and remote branches are in a diverged state, `lg2 pull` fails to do a fast-forward
# merge, even though the history allows it. Using fetch + merge explicitly handles this.
#
# Divergent branch scenario:
#    Remote: A---B---C---D (origin/main)
#                     \
#    Local:            E---F (main, HEAD)
#
# After fetch + merge --no-commit, a fast-forward merge is performed:
#    Result: A---B---C---D---E---F (main, HEAD)
#                                  (origin/main)
#
# This is what `lg2 pull` should do but doesn't, so we do it manually.

if ! lg2 fetch origin; then
    print_msg "${RED}Error: Fetch failed${NO_COLOR}"
    cd "$ORIGINAL_DIR"
    exit 1
fi

if ! lg2 merge --no-commit origin; then
    print_msg "${RED}Error: Merge failed. You may need to resolve conflicts.${NO_COLOR}"
    print_msg "${YELLOW}Run 'lg2 status' to see what needs attention${NO_COLOR}"
    cd "$ORIGINAL_DIR"
    exit 1
fi

print_msg "${GREEN}Pull (fetch + merge) completed successfully${NO_COLOR}"

LOCAL=$(lg2 rev-parse refs/heads/main 2>/dev/null)
REMOTE=$(lg2 rev-parse refs/remotes/origin/main 2>/dev/null || echo "")

if [ -z "$REMOTE" ]; then
    print_msg "${YELLOW}No upstream branch set, pushing to origin...${NO_COLOR}"
    if ! lg2 push -u origin; then
        print_msg "${RED}Error: Push failed${NO_COLOR}"
        cd "$ORIGINAL_DIR"
        exit 1
    fi
    print_msg "${GREEN}Push completed successfully${NO_COLOR}"
elif [ "$LOCAL" != "$REMOTE" ]; then
    print_msg "${YELLOW}Pushing changes to remote...${NO_COLOR}"
    if ! lg2 push origin; then
        print_msg "${RED}Error: Push failed${NO_COLOR}"
        cd "$ORIGINAL_DIR"
        exit 1
    fi
    print_msg "${GREEN}Push completed successfully${NO_COLOR}"
else
    print_msg "${GREEN}Already up to date with remote${NO_COLOR}"
fi

cd "$ORIGINAL_DIR"

print_msg "${GREEN}✓ Git sync completed successfully${NO_COLOR}"

[holzschu]

You mentioned that exit doesn't close the app, I understand this, and I want to highlight that this was not my original intent.

As you can see in the video I have uploaded above... exit is failing to close the existent window on an iPhone.

I see that you say:

It closes the current window on an iPad (which is the same as ending the app if there is only one window open).

...is this not what happens on an iPhone?

There is no way (that I know of) to close a window on iPhone. It's a possibility that only exists on iPads.

[saiki-k]

I see, thanks for the clarification. So, essentially, there is no way to destroy the history, and instance of a-Shell on iPhone, correct?

Nonetheless, thanks a lot for your time on this, I really appreciate it. I will try the TestFlight version as soon as is possible, and I will add any relevant updates here.

[saiki-k]

So, I have tried the TestFlight version, and still, every alternate Shortcut invocation involving lg2 (mostly lg2 status) fails with a segmentation fault, and it keeps happening until I manually open and close a-Shell.

I will try to chalk up a demo (an example repo, shortcut, etc...) and a detailed walkthrough, soon, so you have better visibility on what is happening, and probably you can use it to reproduce this exact issue on your end.

[saiki-k]

@holzschu I have tried to add the steps to reproduce the issue I have described, in as much detail as possible. I confirm that I have tested this both on the AppStore and the TestFlight versions, and I'm on iOS Version 26.1

Please let me know if there is anything else that you need, and I would be happy to help.

---

Steps to reproduce segmentation fault issues with a-Shell iOS Shortcuts using lg2

1. Create a new git repository on GitHub; from the GitHub repo page / interface, add the lg2_sync.sh script under meta/scripts, and commit the addition

• For convenience, you can simply fork the saiki-k/lg2-sync repository.
• Please ensure that you update GIT_CONFIG_USER_NAME, and GIT_CONFIG_USER_EMAIL variables found inside the meta/scripts/lg2_sync.sh script, and commit (+ push) those changes. You can do this directly from the GitHub interface without having to clone the repository locally.
• Skip Steps 2, and 3, if the relevant SSH configurations are already in place, in your a-Shell.

2. Open a-Shell and create a new SSH keypair (if it doesn't already exist) with the relevant email

ssh-keygen -t ed25519 -C "example@email.com"

3. Copy the public key and add it to GitHub, to enable remote git ops.

cat ~/Documents/.ssh/id_ed25519.pub | pbcopy

• In a browser, go to GitHub → Settings → SSH and GPG keys → New SSH key.
• Paste the public key and save it.

4. Create a new folder in your iPhone under On My iPhone, say GitRepos

5. Run the pickFolder command and select the GitRepos folder (a-Shell will mount this folder in the a-Shell environment, adding a bookmark for it)

pickFolder

• When the iOS file picker opens, select On My iPhone → GitRepos.
• Tap Open

6. Clone the repo

lg2 clone git@github.com:your-github-username/lg2-sync.git "lg2-sync"

• Choose SSH key 1 and enter its password (press Enter if no password).
• After the clone is done, a-Shell may suggest running config commands - you can skip these as the sync script handles them.

8. Run the sync script (this will automatically add any needed configurations)

sh lg2-sync/meta/scripts/lg2_sync.sh

• Type y to add GitHub to known hosts.

9. Download the lg2 Sync iOS Shortcut

10. Add/Edit a file in the repo from your PC or elsewhere, and commit (+ push) the addition/update

• Again, it is simpler to do this directly via the GitHub interface.
• Back on the iPhone Shortcuts app, run the above shortcut (Step 9) to sync the changes from the remote.

11. If it doesn't already happen, repeat Step 10, one (or a couple) more time(s), and you should see the segmentation fault errors in the shortcut's output (from a-Shell)

• If you open and close the a-Shell app, and re-run the shortcut, it should work just fine.

[holzschu]

Hi,
I'm having a look right now. There are a lot of steps involved, and I'm trying to work out the most important ones.
My guess is that one important thing is that the repository is outside of a-Shell's own folder, but that cannot be the only issue because other users have repositories outside of a-Shell's own folder.

I've tried running changes on a repository that I have already cloned, doing changes on both sides, doing add, push, pull, commits... and lg2 status never causes a segmentation fault (so far). I am not using your script because I am trying to keep track of the commands that are being run. My next step is to try with your script.

[holzschu]

On the other hand, lg2 status is not printing any useful information beyond "On branch master", which is probably connected to your issue.

[saiki-k]

That's correct, holzchu, it is indeed a directory outside a-Shell which is "mounted" with pickFolder.

My suspicion is that a combination of the above fact + this implementation of lg2 probably not cleaning after itself well after running through an iOS shortcut, is what is causing the segfault errors.

While the (reproduction) steps above are detailed, I am confident that setting it up should not take more than a few minutes and it is the quickest way to get to the segmentation fault error state.

[holzschu]

My problem (for the next time) is that the steps above are too detailed: most of it are instructions on how to set a github repository. It is really difficult to extract the relevant steps from this list.

So, I kept trying and never got to the point where lg2 status causes a segmentation fault. I used your script and 1) it produced an interesting error, and 2) it still does not make lg2 status cause a segmentation fault.

The error was caused by the "lg2 push -u origin" line.

[~Documents_2/a-Shell-commands.git]$ sh ./lg2_sync.sh 
./lg2_sync.sh: 20: cd: can't cd to /private/var/mobile/Containers/Data/Application/5ABE5D77-E896-424F-A572-80FB970EFAC3/Documents/a-Shell-commands.git/../..
Starting git sync for the vault "" on a-Shell...
Checking status...
Local changes detected, staging files...
Committing changes...
Changes committed successfully
Pulling changes from remote...
Fetching origin for repo 0x101654f80

Host: github.com
Public key hashes:
MD5: e5mBHkyRpQ1aLi6AEz8kyg==
SHA-1: M1irXdPjBsRhyED3SH6TtpfjBgA=
SHA-256: p2QAMXNIC1TJYWeIOttrVc98/R1BUFWu3/LiyKgUfQM=

There are 24 known hosts...
Host github.com is in known_hosts!
SSH authentication: Using private key: ~/Documents/.ssh/id_rsa
Received 0/0 objects in 0bytes
Already up-to-date
Pull (fetch + merge) completed successfully
No upstream branch set, pushing to origin...
No refspecs given. Pushing: refs/heads/master

Host: github.com
Public key hashes:
MD5: e5mBHkyRpQ1aLi6AEz8kyg==
SHA-1: M1irXdPjBsRhyED3SH6TtpfjBgA=
SHA-256: p2QAMXNIC1TJYWeIOttrVc98/R1BUFWu3/LiyKgUfQM=

There are 24 known hosts...
Host github.com is in known_hosts!
SSH authentication: Using private key: ~/Documents/.ssh/id_rsa
pushed
Error: No branch for destination of refs/heads/master
Can't make refs/heads/master track refs/heads/master.
 This may be because one of the given refspecs is formatted incorrectly.
These are some example refspecs:
   +refs/heads/localbranch1:refs/remotes/origin/make_it_track_this
        Here, the '+' means we're forcing the update.
   refs/remotes/origin/somebranch
        Updates somebranch with the contents of this branch,  but doesn't force it.
  You can also try `lg2 branch -u 'refs/heads/master'`, which sets the current branch's upstream to refs/heads/master.
Bad news:
 no error
Error: Push failed
[~Documents_2/a-Shell-commands.git]$ lg2 status
# On branch master
[~Documents_2/a-Shell-commands.git]$ 

[holzschu]

I also tried with the Shortcut, I'm still not able to reproduce your issue (which makes sense, the Shortcut does not change anything). I need more specific instructions on how to reproduce this issue, or more information: does lg2 status write anything before "Segmentation fault"?

[saiki-k]

My apologies for the inconvenience. You don't need to create a new repository if that wasn't clear, you can just clone the one mentioned above. And as I mentioned, the segmentation fault happens when the script is run through a shortcut (which I have linked in the details).

I also noticed that you are running the script from the root, it was setup in a way that it has to be two directories below the root of the repository (excerpted from the current setup I made) -- not sure if you have made any changes to this.

The shortcut runs without any issue the first time (or first couple of times in some instances, again as mentioned in the details); the segmentation faults start happening on subsequent runs until a-Shell is manually closed.

I understand that your time is limited, and please feel free to close the issue if you are not equipped to address this at the moment.

However, if you are still interested in getting to the bottom of this, I will block sometime to make a recording, and probably simplify the repo a bit more, with simpler reproducibility instructions...

[saiki-k]

Here is a short recording of the issue. Please notice the failed state of the Shortcut; and once I manually open and close a-Shell it works fine again!

lg2_issues_on_a-Shell.mp4

Please feel free to let me know if you need anything more from me.

[holzschu]

Thanks for the video. If I look at the command output and at your script, it seems like the segmentation fault happens in the call to lg2 push -u origin. In that case, the issue is similat to #667 (but please keep yours open as it has relevant information).

I don't think the localisation or the Shortcut is the issue; it has to be in the specific conflicts created between the two versions of the repository. Simple conflicts created by editing files on both ends are not enough.

Update: after thinking about it, that's not the right explanation. Your videos and descriptions show clearly that there is a memory re-initialization issue. But it only happens after several runs of lg2. In that case, it would be a different issue from #667.

I wonder if the issue can happen if you're only editing from the phone (without conflicts from the other end), just running your script after edits.

Also, do you have an idea about how many calls to your Shortcut are required before the issue happens? Is that around 5 calls, 10 calls, 50 ?