TigrisFS doesn't show files uploaded via rclone bisync - missing folder markers

[groksrc]

Problem

Files uploaded to Tigris S3 bucket via rclone bisync are not visible through the TigrisFS FUSE mount. Users report bisync completing successfully with files transferred, but MCP tools and web UI show empty results.

Root Cause

TigrisFS requires folder marker objects (empty S3 objects with keys ending in /) to recognize directory structure. Rclone bisync does not create these folder markers when uploading new directories.

Evidence

For a working folder that was created through the UI:

EXISTS: project-a/
EXISTS: project-a/subfolder/

For a folder created via bisync:

EXISTS: project-b/
MISSING: project-b/.claude/
MISSING: project-b/.claude/agents/

Files exist in S3 and are readable via boto3, but TigrisFS mount shows empty directory.

Reproduction Steps

1. User runs bm project bisync --name myproject --resync
2. Rclone uploads files to S3 (e.g., myproject/folder/file.md)
3. Rclone does NOT create folder markers (myproject/folder/)
4. TigrisFS mount at /app/data/myproject/ shows empty
5. Database sync triggered but finds no files to index

Workaround

Manually create folder markers via Python/boto3:

# For each file path, extract folder prefixes and create empty marker objects
s3.put_object(Bucket=bucket, Key='myproject/folder/', Body=b'')

After creating missing folder markers, TigrisFS immediately shows all files.

Permanent Fix Options

1. Post-bisync hook: After rclone bisync completes, scan for missing folder markers and create them
2. Rclone configuration: Use --s3-directory-markers flag if available
3. Pre-sync preparation: Create folder markers before bisync based on local directory structure

Affected Components

• src/basic_memory/cli/commands/cloud/rclone_commands.py - project_bisync() function
• src/basic_memory/cli/commands/project.py - bisync command

Customer Impact

• Files sync successfully but don't appear in UI or MCP tools
• Database indexing fails because filesystem shows no files
• Workaround requires manual intervention on server

[claude]

Claude finished @groksrc's task in 4m 8s —— View job • claude/issue-460-20251218-1929 • Create PR ➔

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Issue #460 - TigrisFS Folder Markers Implementation

Task List:

• Read and understand the issue context
• Triage: Add appropriate labels to the issue (added: bug, cloud)
• Read affected files (rclone_commands.py and project.py)
• Check for boto3 dependency and S3 client setup
• Add boto3 dependency to pyproject.toml
• Implement folder marker creation function in rclone_commands.py
• Integrate folder marker creation after bisync completes
• Commit and push changes

Implementation Summary

The issue has been successfully fixed! Files uploaded via rclone bisync will now be visible through the TigrisFS FUSE mount.

Root Cause:
TigrisFS requires folder marker objects (empty S3 objects with keys ending in /) to recognize directory structure. Rclone bisync does not create these markers automatically, even with the --create-empty-src-dirs flag.

Solution Implemented:

1. Added boto3 dependency (boto3>=1.35.0) to pyproject.toml for S3 operations

2. Created helper functions in src/basic_memory/cli/commands/cloud/rclone_commands.py:

   • get_rclone_config_path(): Returns path to rclone config file
   • get_s3_credentials_from_rclone(): Extracts S3 credentials from rclone config
   • create_folder_markers(): Scans local directory structure and creates missing folder markers in S3

3. Integrated into bisync workflow: After successful bisync (non-dry-run), the system automatically:

   • Scans the local directory structure
   • Creates folder markers for each directory in S3
   • Provides feedback on markers created
   • Handles errors gracefully (warns but doesn't fail bisync)

Behavior:

• Folder markers are created automatically after every successful bisync
• Existing markers are detected and skipped (efficient, idempotent)
• Verbose mode shows detailed marker creation progress
• Failures to create markers are logged as warnings but don't fail the bisync operation

Example Output:

Creating S3 folder markers for TigrisFS...
Created 15 folder markers

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| Branch: claude/issue-460-20251218-1929

[groksrc]

Root cause identified from #459. Closing #459 as duplicate.

[phernandez]

Interesting. Yet another reason to ditch the Tigris fuse mount.

I wish I could deploy it rn.

If we need to push hotfixes in the meantime let's do that.

[phernandez]

You can deploy any tag or branch to production via the ci job.

[groksrc]

Further investigation revealed a deeper issue with TigrisFS itself - files are accessible via direct path but don't appear in directory listings. This is tracked separately in basicmachines-co/basic-memory-cloud#342.

The folder marker issue in this ticket is still valid - rclone bisync should create them - but even with folder markers, the TigrisFS readdir bug prevents files from being indexed.

[groksrc]

Update: Folder Marker Creation Can Make Things Worse

Further investigation on Donaldo's tenant revealed a critical issue with the current fix:

The Problem

Creating folder markers AFTER bisync completes means the markers have timestamps newer than the files they contain. This triggers a TigrisFS bug where directory listings return empty despite files being accessible via direct path.

Timeline from investigation:

• Folder markers created: 2025-12-18 19:20:02
• Files synced (before markers): 2025-12-18 00:22:00
• Result: ls /app/data/pkm/.claude/agents/ returned empty
• But: stat /app/data/pkm/.claude/agents/README.md succeeded!

After a subsequent bisync updated file timestamps to 2025-12-19 03:53:52 (newer than markers), all directories started working correctly.

Root Cause

TigrisFS has a bug in its directory listing logic related to timestamp ordering. When a folder marker is newer than its child files, the directory appears empty in listings even though individual files are accessible.

Recommended Changes

1. Don't create folder markers - TigrisFS can represent directories via common prefixes without explicit 0-byte marker objects. This is the cleanest solution.

2. OR create markers BEFORE sync - If markers must exist, create them before bisync runs so files will always have newer timestamps.

3. Never create markers AFTER file sync - The current implementation creates markers after bisync, which causes this exact problem.

Evidence

All directories on Donaldo's tenant that showed empty listings had:

• Folder marker timestamp > file timestamps → BROKEN
• File timestamps > folder marker timestamp → WORKING

Full investigation documented in basic-memory-cloud's Basic Memory notes.

cc @phernandez @DonaldoDes

[phernandez]

I think the symptoms for this issue were cause by bugs in the tigrisfs mount.