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chore: initialize beads issue tracking
Adds git-synced issue tracking for persistent work state across sessions. Includes custom merge driver config for JSONL conflict resolution. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]>
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‎.beads/.gitignore‎

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# SQLite databases
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*.db
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*.db?*
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*.db-journal
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*.db-wal
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*.db-shm
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# Daemon runtime files
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daemon.lock
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daemon.log
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daemon.pid
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bd.sock
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# Legacy database files
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db.sqlite
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bd.db
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# Merge artifacts (temporary files from 3-way merge)
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beads.base.jsonl
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beads.base.meta.json
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beads.left.jsonl
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beads.left.meta.json
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beads.right.jsonl
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beads.right.meta.json
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# Keep JSONL exports and config (source of truth for git)
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!issues.jsonl
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!metadata.json
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!config.json

‎.beads/.local_version‎

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0.29.0

‎.beads/README.md‎

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# Beads - AI-Native Issue Tracking
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Welcome to Beads! This repository uses **Beads** for issue tracking - a modern, AI-native tool designed to live directly in your codebase alongside your code.
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## What is Beads?
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Beads is issue tracking that lives in your repo, making it perfect for AI coding agents and developers who want their issues close to their code. No web UI required - everything works through the CLI and integrates seamlessly with git.
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**Learn more:** [github.com/steveyegge/beads](https://github.com/steveyegge/beads)
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## Quick Start
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### Essential Commands
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```bash
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# Create new issues
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bd create "Add user authentication"
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# View all issues
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bd list
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# View issue details
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bd show <issue-id>
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# Update issue status
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bd update <issue-id> --status in_progress
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bd update <issue-id> --status done
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# Sync with git remote
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bd sync
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```
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### Working with Issues
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Issues in Beads are:
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- **Git-native**: Stored in `.beads/issues.jsonl` and synced like code
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- **AI-friendly**: CLI-first design works perfectly with AI coding agents
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- **Branch-aware**: Issues can follow your branch workflow
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- **Always in sync**: Auto-syncs with your commits
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## Why Beads?
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✨ **AI-Native Design**
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- Built specifically for AI-assisted development workflows
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- CLI-first interface works seamlessly with AI coding agents
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- No context switching to web UIs
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🚀 **Developer Focused**
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- Issues live in your repo, right next to your code
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- Works offline, syncs when you push
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- Fast, lightweight, and stays out of your way
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🔧 **Git Integration**
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- Automatic sync with git commits
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- Branch-aware issue tracking
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- Intelligent JSONL merge resolution
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## Get Started with Beads
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Try Beads in your own projects:
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```bash
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# Install Beads
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curl -sSL https://raw.githubusercontent.com/steveyegge/beads/main/scripts/install.sh | bash
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# Initialize in your repo
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bd init
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# Create your first issue
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bd create "Try out Beads"
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```
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## Learn More
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- **Documentation**: [github.com/steveyegge/beads/docs](https://github.com/steveyegge/beads/tree/main/docs)
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- **Quick Start Guide**: Run `bd quickstart`
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- **Examples**: [github.com/steveyegge/beads/examples](https://github.com/steveyegge/beads/tree/main/examples)
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---
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*Beads: Issue tracking that moves at the speed of thought* ⚡

‎.beads/config.yaml‎

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# Beads Configuration File
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# This file configures default behavior for all bd commands in this repository
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# All settings can also be set via environment variables (BD_* prefix)
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# or overridden with command-line flags
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# Issue prefix for this repository (used by bd init)
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# If not set, bd init will auto-detect from directory name
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# Example: issue-prefix: "myproject" creates issues like "myproject-1", "myproject-2", etc.
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# issue-prefix: ""
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# Use no-db mode: load from JSONL, no SQLite, write back after each command
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# When true, bd will use .beads/issues.jsonl as the source of truth
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# instead of SQLite database
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# no-db: false
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# Disable daemon for RPC communication (forces direct database access)
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# no-daemon: false
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# Disable auto-flush of database to JSONL after mutations
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# no-auto-flush: false
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# Disable auto-import from JSONL when it's newer than database
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# no-auto-import: false
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# Enable JSON output by default
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# json: false
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# Default actor for audit trails (overridden by BD_ACTOR or --actor)
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# actor: ""
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# Path to database (overridden by BEADS_DB or --db)
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# db: ""
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# Auto-start daemon if not running (can also use BEADS_AUTO_START_DAEMON)
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# auto-start-daemon: true
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# Debounce interval for auto-flush (can also use BEADS_FLUSH_DEBOUNCE)
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# flush-debounce: "5s"
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# Git branch for beads commits (bd sync will commit to this branch)
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# IMPORTANT: Set this for team projects so all clones use the same sync branch.
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# This setting persists across clones (unlike database config which is gitignored).
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# Can also use BEADS_SYNC_BRANCH env var for local override.
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# If not set, bd sync will require you to run 'bd config set sync.branch <branch>'.
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# sync-branch: "beads-sync"
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# Multi-repo configuration (experimental - bd-307)
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# Allows hydrating from multiple repositories and routing writes to the correct JSONL
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# repos:
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# primary: "." # Primary repo (where this database lives)
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# additional: # Additional repos to hydrate from (read-only)
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# - ~/beads-planning # Personal planning repo
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# - ~/work-planning # Work planning repo
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# Integration settings (access with 'bd config get/set')
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# These are stored in the database, not in this file:
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# - jira.url
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# - jira.project
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# - linear.url
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# - linear.api-key
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# - github.org
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# - github.repo

‎.beads/issues.jsonl‎

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{"id":"sp_validation-15j","title":"Review and commit uncommitted ellipticity-suffix work","description":"7 files with uncommitted changes: cosmo_val.py, rho_tau.py, cosmosis_fitting.py, cosmic shear paper configs. Appear to be bug fixes (bin construction, file naming, covariance).","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-16T17:31:10.777988207+01:00","updated_at":"2025-12-16T20:08:21.251378337+01:00","closed_at":"2025-12-16T20:08:21.251378337+01:00"}
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{"id":"sp_validation-1en","title":"Merge PR #165 (catalog path standardization)","description":"PR approved by Lisa and Sacha since Oct/Nov. Ready to merge for 6 weeks. Run: gh pr merge 165 --merge","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-16T17:31:16.438050654+01:00","updated_at":"2025-12-16T17:31:16.438050654+01:00","dependencies":[{"issue_id":"sp_validation-1en","depends_on_id":"sp_validation-d4d","type":"blocks","created_at":"2025-12-16T17:31:37.693645344+01:00","created_by":"daemon"}]}
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{"id":"sp_validation-1en","title":"Merge PR #165 (catalog path standardization)","description":"PR approved by Lisa and Sacha since Oct/Nov. Ready to merge for 6 weeks. Run: gh pr merge 165 --merge","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-16T17:31:16.438050654+01:00","updated_at":"2025-12-16T20:34:02.694916064+01:00","closed_at":"2025-12-16T20:34:02.694916064+01:00","dependencies":[{"issue_id":"sp_validation-1en","depends_on_id":"sp_validation-d4d","type":"blocks","created_at":"2025-12-16T17:31:37.693645344+01:00","created_by":"daemon"}]}
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{"id":"sp_validation-7ww","title":"PR #165: data_base_dir parameter removed (breaking)","description":"CosmologyValidation.__init__() no longer accepts data_base_dir. Paths now absolute in cat_config.yaml. May break external scripts. Approved by Lisa/Sacha - presumably validated for their use cases.","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-16T20:19:19.480910265+01:00","updated_at":"2025-12-16T20:19:19.480910265+01:00"}
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{"id":"sp_validation-d4d","title":"Run test suite and validate","description":"After pytest fix, run full test suite to validate ellipticity-suffix changes.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-16T17:31:13.621333151+01:00","updated_at":"2025-12-16T17:41:14.552278446+01:00","closed_at":"2025-12-16T17:41:14.552278446+01:00","dependencies":[{"issue_id":"sp_validation-d4d","depends_on_id":"sp_validation-es5","type":"blocks","created_at":"2025-12-16T17:31:37.617063707+01:00","created_by":"daemon"}]}
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{"id":"sp_validation-es5","title":"Fix pytest config (remove --pydocstyle)","description":"pyproject.toml line 81 has deprecated --pydocstyle flag. Tests won't run until fixed.","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-12-16T17:31:07.933332484+01:00","updated_at":"2025-12-16T17:37:12.452426193+01:00","closed_at":"2025-12-16T17:37:12.452426193+01:00"}
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{"id":"sp_validation-gco","title":"Fix pyccl Cosmology.get API deprecation","description":"test_ccl_to_camb_basic and test_camb_backend fail due to pyccl API change. Cosmology object no longer has .get() method.","status":"open","priority":2,"issue_type":"bug","created_at":"2025-12-16T17:41:17.33553874+01:00","updated_at":"2025-12-16T17:41:17.33553874+01:00"}
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{"id":"sp_validation-o97","title":"Add nellbins suffix to pseudo-Cl output filenames","description":"For reproducibility, output files should include binning params. Deferred pending binning resolution in PR #168.","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-16T18:40:03.290961433+01:00","updated_at":"2025-12-16T18:40:03.290961433+01:00"}
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{"id":"sp_validation-rq0","title":"Add SP_v1.4.5_glass_mock to test allow-list or fix path","description":"test_catalog_paths_exist fails: SP_v1.4.5_glass_mock shear file missing. Either add to allow-list or update path in cat_config.yaml","status":"open","priority":2,"issue_type":"bug","created_at":"2025-12-16T17:42:59.575066932+01:00","updated_at":"2025-12-16T17:42:59.575066932+01:00"}
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{"id":"sp_validation-rq0","title":"Add SP_v1.4.5_glass_mock to test allow-list or fix path","description":"test_catalog_paths_exist fails: SP_v1.4.5_glass_mock shear file missing. Either add to allow-list or update path in cat_config.yaml","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-12-16T17:42:59.575066932+01:00","updated_at":"2025-12-16T20:34:24.146324717+01:00","closed_at":"2025-12-16T20:34:24.146324717+01:00"}
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{"id":"sp_validation-xop","title":"Coordinate NmtBin linear binning with PR #168","description":"Deferred from ellipticity-suffix. Changes to NmtBin constructor, n_bands vs n_ell_bins, dynamic step. Sacha's PR #168 has 'To be implemented correctly' comment. Coordinate there.","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-16T18:40:00.538355923+01:00","updated_at":"2025-12-16T18:40:00.538355923+01:00"}

‎.beads/metadata.json‎

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{
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"database": "beads.db",
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"jsonl_export": "issues.jsonl"
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}

‎.gitattributes‎

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# Use bd merge for beads JSONL files
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.beads/issues.jsonl merge=beads

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