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BUG-HUNT: [database] Alembic migrations are unnecessarily complex and risky #2418

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opened 2026-04-03 17:41:17 +00:00 by freemo · 1 comment
freemo commented 2026-04-03 17:41:17 +00:00
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Metadata

  • Branch: fix/database-alembic-migrations-risky-patterns
  • Commit Message: fix(database): refactor risky drop-and-recreate migration patterns to safe ALTER TABLE operations
  • Milestone: v3.6.0 (Post-MVP Release)
  • Parent Epic: #1020

Bug Report: [database] — Alembic migrations are unnecessarily complex and risky

Severity Assessment

  • Impact: High. The current migration strategy involves dropping and recreating tables, which can lead to data loss and service downtime during deployments. The complex backfill logic is a source of potential data corruption.
  • Likelihood: High. The complexity is already present in the codebase and will be a recurring problem for future schema changes.
  • Priority: High

Location

  • File: alembic/versions/a5_003_spec_aligned_actions.py, alembic/versions/a5_004_spec_aligned_plans.py, alembic/versions/a5_005_rebaseline_plan_phases.py, alembic/versions/m8_001_align_plans_schema.py

Description

Several Alembic migrations in the alembic/versions directory are unnecessarily complex and risky. They follow a pattern of dropping and recreating tables to alter constraints or columns, which is a dangerous practice in a production environment.

Specifically:

  • a5_003_spec_aligned_actions.py and a5_004_spec_aligned_plans.py drop and recreate tables, which could be avoided with more granular ALTER TABLE statements.
  • a5_005_rebaseline_plan_phases.py rebuilds the v3_plans table to update a CHECK constraint, which is a very heavy-handed approach.
  • m8_001_align_plans_schema.py contains complex backfill logic with a loop that could cause performance issues or fail silently, leading to data inconsistencies.

This approach indicates a lack of understanding of safe database migration practices and puts the application at risk of data loss and extended downtime during upgrades.

Evidence

(Code snippets from the mentioned migration files)

Expected Behavior

Database migrations should be written defensively to preserve data and minimize downtime. This means:

  • Using ALTER TABLE to add, remove, or modify columns and constraints whenever possible.
  • Avoiding dropping and recreating tables unless absolutely necessary (e.g., for a complete schema overhaul).
  • Writing backfill logic that is idempotent, efficient, and robust against edge cases like cycles in hierarchical data.

Actual Behavior

The migrations use a risky drop-and-recreate pattern and contain complex, potentially fragile backfill logic.

Suggested Fix

  • Refactor the identified migrations to use op.alter_column, op.create_check_constraint, op.drop_constraint, etc., to modify the schema without dropping tables.
  • Simplify the backfill logic in m8_001_align_plans_schema.py to be more robust and less prone to infinite loops. Consider using a more declarative approach if possible.

Category

database | consistency

Subtasks

  • Audit all migration files in alembic/versions/ for drop-and-recreate patterns
  • Refactor a5_003_spec_aligned_actions.py to use op.alter_column / op.add_column / op.drop_column instead of table drop-and-recreate
  • Refactor a5_004_spec_aligned_plans.py to use granular ALTER TABLE operations instead of table drop-and-recreate
  • Refactor a5_005_rebaseline_plan_phases.py to update the CHECK constraint on v3_plans without rebuilding the table
  • Refactor backfill logic in m8_001_align_plans_schema.py to be idempotent, efficient, and safe against cycles in hierarchical data
  • Verify all refactored migrations are reversible (downgrade path tested)
  • Tests (Behave): Add/update scenarios covering migration upgrade and downgrade paths
  • Tests (Robot): Add integration test verifying data integrity across migration steps
  • Verify coverage >=97% via nox -s coverage_report
  • Run nox (all default sessions), fix any errors

Definition of Done

This issue is complete when:

  • All subtasks above are completed and checked off.
  • All identified migration files have been refactored to use safe, non-destructive ALTER TABLE operations wherever possible.
  • Backfill logic in m8_001_align_plans_schema.py is idempotent, efficient, and handles edge cases (e.g., cycles in hierarchical data) without risk of infinite loops or silent failures.
  • A Git commit is created where the first line of the commit message matches the Commit Message in Metadata exactly, followed by a blank line, then additional lines providing relevant details about the implementation.
  • The commit is pushed to the remote on the branch matching the Branch in Metadata exactly.
  • The commit is submitted as a pull request to master, reviewed, and merged before this issue is marked done.
  • All nox stages pass.
  • Coverage >= 97%

Automated by CleverAgents Bot
Supervisor: Bug Hunting | Agent: ca-new-issue-creator

## Metadata - **Branch**: `fix/database-alembic-migrations-risky-patterns` - **Commit Message**: `fix(database): refactor risky drop-and-recreate migration patterns to safe ALTER TABLE operations` - **Milestone**: v3.6.0 (Post-MVP Release) - **Parent Epic**: #1020 ## Bug Report: [database] — Alembic migrations are unnecessarily complex and risky ### Severity Assessment - **Impact**: High. The current migration strategy involves dropping and recreating tables, which can lead to data loss and service downtime during deployments. The complex backfill logic is a source of potential data corruption. - **Likelihood**: High. The complexity is already present in the codebase and will be a recurring problem for future schema changes. - **Priority**: High ### Location - **File**: `alembic/versions/a5_003_spec_aligned_actions.py`, `alembic/versions/a5_004_spec_aligned_plans.py`, `alembic/versions/a5_005_rebaseline_plan_phases.py`, `alembic/versions/m8_001_align_plans_schema.py` ### Description Several Alembic migrations in the `alembic/versions` directory are unnecessarily complex and risky. They follow a pattern of dropping and recreating tables to alter constraints or columns, which is a dangerous practice in a production environment. Specifically: - `a5_003_spec_aligned_actions.py` and `a5_004_spec_aligned_plans.py` drop and recreate tables, which could be avoided with more granular `ALTER TABLE` statements. - `a5_005_rebaseline_plan_phases.py` rebuilds the `v3_plans` table to update a CHECK constraint, which is a very heavy-handed approach. - `m8_001_align_plans_schema.py` contains complex backfill logic with a loop that could cause performance issues or fail silently, leading to data inconsistencies. This approach indicates a lack of understanding of safe database migration practices and puts the application at risk of data loss and extended downtime during upgrades. ### Evidence (Code snippets from the mentioned migration files) ### Expected Behavior Database migrations should be written defensively to preserve data and minimize downtime. This means: - Using `ALTER TABLE` to add, remove, or modify columns and constraints whenever possible. - Avoiding dropping and recreating tables unless absolutely necessary (e.g., for a complete schema overhaul). - Writing backfill logic that is idempotent, efficient, and robust against edge cases like cycles in hierarchical data. ### Actual Behavior The migrations use a risky drop-and-recreate pattern and contain complex, potentially fragile backfill logic. ### Suggested Fix - Refactor the identified migrations to use `op.alter_column`, `op.create_check_constraint`, `op.drop_constraint`, etc., to modify the schema without dropping tables. - Simplify the backfill logic in `m8_001_align_plans_schema.py` to be more robust and less prone to infinite loops. Consider using a more declarative approach if possible. ### Category database | consistency ## Subtasks - [ ] Audit all migration files in `alembic/versions/` for drop-and-recreate patterns - [ ] Refactor `a5_003_spec_aligned_actions.py` to use `op.alter_column` / `op.add_column` / `op.drop_column` instead of table drop-and-recreate - [ ] Refactor `a5_004_spec_aligned_plans.py` to use granular `ALTER TABLE` operations instead of table drop-and-recreate - [ ] Refactor `a5_005_rebaseline_plan_phases.py` to update the CHECK constraint on `v3_plans` without rebuilding the table - [ ] Refactor backfill logic in `m8_001_align_plans_schema.py` to be idempotent, efficient, and safe against cycles in hierarchical data - [ ] Verify all refactored migrations are reversible (downgrade path tested) - [ ] Tests (Behave): Add/update scenarios covering migration upgrade and downgrade paths - [ ] Tests (Robot): Add integration test verifying data integrity across migration steps - [ ] Verify coverage >=97% via `nox -s coverage_report` - [ ] Run `nox` (all default sessions), fix any errors ## Definition of Done This issue is complete when: - All subtasks above are completed and checked off. - All identified migration files have been refactored to use safe, non-destructive `ALTER TABLE` operations wherever possible. - Backfill logic in `m8_001_align_plans_schema.py` is idempotent, efficient, and handles edge cases (e.g., cycles in hierarchical data) without risk of infinite loops or silent failures. - A Git commit is created where the **first line** of the commit message matches the Commit Message in Metadata exactly, followed by a blank line, then additional lines providing relevant details about the implementation. - The commit is pushed to the remote on the branch matching the **Branch** in Metadata exactly. - The commit is submitted as a **pull request** to `master`, reviewed, and **merged** before this issue is marked done. - All nox stages pass. - Coverage >= 97% --- **Automated by CleverAgents Bot** Supervisor: Bug Hunting | Agent: ca-new-issue-creator
freemo added this to the v3.6.0 milestone 2026-04-03 17:41:21 +00:00
freemo commented 2026-04-03 18:24:28 +00:00
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Issue triaged by project owner:

  • State: Verified
  • Priority: High — Risky drop-and-recreate migration patterns can cause data loss in production. This is a database safety issue.
  • Milestone: v3.6.0
  • MoSCoW: Should Have — While the migrations work, the risky patterns should be refactored to safe ALTER TABLE operations before any production deployment. Not blocking development but blocking production readiness.
  • Parent Epic: #1020 (Database resource hierarchy restructuring)

Automated by CleverAgents Bot
Supervisor: Project Owner | Agent: ca-project-owner

Issue triaged by project owner: - **State**: Verified - **Priority**: High — Risky drop-and-recreate migration patterns can cause data loss in production. This is a database safety issue. - **Milestone**: v3.6.0 - **MoSCoW**: Should Have — While the migrations work, the risky patterns should be refactored to safe ALTER TABLE operations before any production deployment. Not blocking development but blocking production readiness. - **Parent Epic**: #1020 (Database resource hierarchy restructuring) --- **Automated by CleverAgents Bot** Supervisor: Project Owner | Agent: ca-project-owner
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docs/timeline-update-2026-04-15
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bugfix/m4-plan-diff-correction-stub
pr-9247
docs/timeline-update-2026-04-17
timeline/day-106-2026-04-17-auto-time-1
fix/quality-gates-click82-compat
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fix/issue-6441-session-create-json-output
fix/issue-6331-invariant-add-scope
timeline/day-106-2026-04-16-auto-time-1-v2
spec/auto-arch-23-minor-clarifications
timeline/day-106-2026-04-16-auto-time-2
docs/auto-docs-2-v380-v390
timeline/day-104-2026-04-14-auto-time-1
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auto-docs/changelog-architecture-readme
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chore/timeline-day-105-2026-04-15
docs/timeline-update-2026-04-15-auto-time-1
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benchmark-ci
fix/plan-phase-migration-raw-sql-root-plan-id
auto-arch-12/spec-acms-context-tier-hydrator
timeline/day-106-2026-04-15-auto-time-1
feat/invariant-enforcement-strategize
feat/plan-tree-decision-rendering
feat/plan-correct-revert-append-modes
docs/auto-docs-4-fix-conflicts
docs/auto-docs-1-milestone-docs-v3.0.0-v3.1.0
feat/v3.4.0-acms-lifecycle-policy
pr-9220
fix/a2a-facade-optional-param-validation
feat/ci-guard-llm-secrets
pr-9214
feat/v3.3.0-subplan-status-tracking
feat/v3.3.0-merge-conflict-detection
uat/checkpoint-rollback-merge-tests
fix/pr-review-pool-supervisor-prefix-mismatch
feat/v3.3.0-spawn-subplan-step
auto-time-1-day103-cycle1-session6
feat/v3.8.0-agent-card-endpoint
docs/auto-docs-cycle-24-showcase-nav
auto-inf-3-consolidate-behave-fixtures
fix/issue-7663-docs-writer-missing
auto-time-1-day103-cycle2
docs/timeline-day-104-auto-time-1
auto-arch-16/spec-xml-prompt-injection-mitigation
bugfix/m4-invariant-persistence
uat-a2a-facade-tests-v350
bugfix/m3-behave-parallel-failed-chunk-logs
bugfix/7664-automation-tracking-label-requirements
docs/auto-time-1-timeline-update-2026-04-14
docs/auto-docs-1-milestone-v3-updates
fix/issue-6344-plan-execute-rich-output
docs/action-config-schema-api
fix/bug-hunt-supervisor-nonexistent-file-preflight
fix/retry-policy-model-missing-fields
docs/validation-gate-empty-run-guard
auto-arch-15/spec-retry-policy-canonical-fields
docs/lockservice-advisory-locking
docs/changelog-plan-fix-4197
spec/milestone-plan-section
docs/update-changelog-recent-features
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timeline/day-104-2026-04-14-cycle2
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docs/auto-docs-cycle-1-2026-04-12
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docs/developer-setup-guide
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spec/resource-event-types-clarification
auto-docs-4/changelog-and-observability
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docs/a2a-protocol-autonomy-hardening
auto-arch-9/spec-v3.8.0-milestone-plan
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test/create-scripts
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timeline/day-104-2026-04-14
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spec/three-way-merge-strategy-v3.3.0
spec/checkpoint-system-v3.3.0
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pr-8289
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docs/auto-docs-1-milestone-overview
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feat/issue-6361-shell-safety-service-tui
spec/architecture-cycle-25-new-features
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docs/timeline-day-102-2026-04-12
docs/cycle-2-git-worktree-acms-hydrator
spec/arch-sandbox-cleanup-discovery
docs/timeline-day96-2026-04-08
docs/auto-docs-cycle-11
spec/fix-sandbox-strategy-protocol-name
spec/arch-acms-tier-hydration
fix/v3.4.0/context-settings-defaults
docs/add-example-repl-and-actor-run
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docs/timeline-day-97
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docs/timeline-day99-2026-04-09-v2
docs/auto-docs-cycle-2-worktree-acms
spec/architecture-v3.8.0-milestone-plan
docs/api-lsp-acms-reference
improvement/agent-bug-hunt-pool-supervisor-yaml-syntax-fix
spec/project-delete-deleted-at-field
spec/architecture-provider-registry-tui-materializer
spec/document-reconciliation-blocked-error-5942
fix/issue-7482-git-log-injection
spec/devcontainer-auto-discovery-schema
feat/issue-6350-conversation-content-pruning
docs/update-module-guides-2026-04-10
timeline/day-100-2026-04-10-auto-time-cycle1
timeline/day-99-2026-04-09-auto-time-v2
docs/cycle-3-module-guides
timeline/day-99-2026-04-09-auto-time
pr-4226
spec/additional-llm-providers-gemini-groq-cohere-together-ollama-mistral
spec/document-context-tier-hydrator-6175
docs/timeline-day99-2026-04-09
spec/invariant-cli-clarifications
docs/add-example-project-init-and-context-management
spec/reconciliation-blocked-error-documentation
spec/fix-invariant-precedence-reference-5861
spec/fix-plan-correct-accepts-plan-id-5558
spec/fix-validation-attach-synopsis-5328
docs/timeline-day-99-cycle-1
docs/timeline-day-99-cycle-2
fix/actor-context-list-regex-arg
docs/timeline-day-99-cycle-3
spec/arch-security-mode-init
docs/auto-docs-cycle-9-updates
fix-resource-fix-resource-remove-to-check-correct-edge-table
feat/issue-6434-tui-env-var-expansion
fix/issue-6321-plan-prompt-timing-field
fix/issue-6322-resource-add-url-flag
feat/issue-6348-sessions-screen
spec/plan-show-command
temp
feat/harden-label-restrictions-1775753628
spec/invariant-reconciliation-failure-behavior
spec/add-reconciliation-failure-behavior-5942
spec/architecture-corrections-cycle3
spec/checkpoint-trigger-names-and-config-key-fix
spec/fix-ai-provider-interface-5801
spec/azure-api-version-default-update
docs/auto-docs-writer-cycle1-labels
spec/fix-resource-type-yaml-format-5622
spec/add-plan-revert-resume-commands-5574
docs/auto-docs-cycle-1-2026-04-09
spec/plan-correct-plan-id-or-decision-id-5558
spec/fix-subgraph-node-actor-ref-field-5427
issue/5284-master-ci-fix
timeline/day-99-2026-04-09-v2
merge-me
docs/session-3377-initial-docs-update
fix/llm-provider-subpackage-exports
spec/arce-acronym-and-tui-keybinding-fixes
spec/architecture-corrections-cycle2
spec/architecture-corrections-cycle1
docs/cycle-1-updates
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docs/session-4940-2026-04-08-cycle1
spec/architecture-milestone-plan-v3.2-v3.7
docs/session-4743-2026-04-08-cycle1
docs/timeline-day-98
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docs/timeline-day98-2026-04-08-v2
docs/add-example-action-and-plan-management
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docs/ca-docs-writer-v3.8.1-2026-04-05
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improvement/agent-arch-guard-clone-failure-handling
improvement/agent-test-infra-health-spam-fix-v2
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docs/timeline-day95-final-2026-04-05
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docs/add-lsp-api-and-changelog-2026-04-05
fix/tool-registry-validation-type-discriminator
docs/v3.7.0-documentation-update
docs/ca-docs-writer-2026-04-05-cycle2
fix/invariant-set-merge-action-scope
docs/unreleased-feature-docs
fix/concurrency-cost-tracker-record-usage-race-condition
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docs/update-changelog-mcp-plan-ci-2026-04-05
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docs/timeline-day95-refresh-2026-04-05
improvement/agent-mandatory-labels-tracking-issues
docs/api-domain-providers-changelog-2026-04-05
docs/ca-docs-writer-2026-04-05
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fix/skill-add-include-validation
docs/timeline-day-95-2026-04-05-update3
docs/timeline-day-95-2026-04-05-update2
docs/ci-incident-runbook-2597
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When an epic or legendary is in review it must be signed off by owner, tech lead, and scrum master before being marked as completed.

  
Signed-off: Tech Lead
When an epic or legendary is in review it must be signed off by owner, tech lead, and scrum master before being marked as completed.

  
Spike
A ticket for learning a tool or technology that is needed to be able to do future planning and design.

  
State
Completed
 The ticket has been fully implemented, completed, and merged with the source code. This label should only be applied once a ticket is closed.

  
State
Duplicate
 A ticket that represents the same content as an existing ticket.

  
State
In Progress
 A ticket that is actively being developed.

  
State
In Review
 A ticket that has had some code completed to implement but is waiting to pass peer review and is not yet merged in.

  
State
Paused
 This ticket's work started but wasn't finished. It's on hold (likely in a feature branch) and will be resumed later, either due to a blocker or a delay.

  
State
Unverified
 All new tickets start in this state. A developer may set it to show the ticket is unverified. This means we haven't agreed to work on it. It will either move to a verified state or be closed as wontdo.

  
State
Verified
 The issue has been verified by a developer as legitimate. It will be worked on and verified tickets are now considered part of the backlog.

  
State
Wont Do
 This ticket has been decided it wont be done. This may mean the bug has been determined to not be real (cant verify) or the feature is one we have decided we dont want to adopt.

  
Type
Automation
 Any edits or discussion about the AI automated coding system.

  
Type
Bug
 Something that doesnt work as intended.

  
Type
Discussion
 Anytime a ticket represents a discussion about a subject and doesnt fall into one of the other categories.

  
Type
Documentation
 An error or improvement needed in the documentation.

  
Type
Epic
 Any first tier epic. That is, an epic which contains only issues as children and will not have sub-epics.

  
Type
Feature
 Some new functionality not present.

  
Type
Legendary
 A type of Epic which will contain other Epics.

  
Type
Refactor
 A code change that restructures existing code without changing its external behavior.

  
Type
Support
 Someone needs help using the project.

  
Type
Task
 A generic task that doesnt fit into the other type categories.

  
Type
Testing
 Work exclusively focusing on fixing or expanding testing.

No labels
auto/needs-reevaluation
controller-managed
auto/blocked-by-deps
auto/ci-timeout
auto/claimed-implementer
auto/claimed-merge
auto/claimed-reviewer
auto/driver-down
auto/invariant-violation
auto/last-attempt-tier-0
auto/last-attempt-tier-1
auto/last-attempt-tier-2
auto/last-attempt-tier-min
Automation Tracking
auto/needs-conflict-resolution
auto/needs-implementer
auto/postmortem
auto/ready-to-merge
auto/restart-throttled
auto/revert
auto/sentinel
auto/stale-inactivity
auto/unstable
Blocked
Bounty
$100
Bounty
$1000
Bounty
$10000
Bounty
$20
Bounty
$2000
Bounty
$250
Bounty
$50
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$500
Bounty
$5000
Bounty
$750
MoSCoW
Could have
MoSCoW
Must have
MoSCoW
Should have
Needs Feedback
Points
1
Points
13
Points
2
Points
21
Points
3
Points
34
Points
5
Points
55
Points
8
Points
88
Priority
Backlog
Priority
CI Blocker
Priority
Critical
Priority
High
Priority
Low
Priority
Medium
Signed-off: Owner
Signed-off: Scrum Master
Signed-off: Tech Lead
Spike
State
Completed
State
Duplicate
State
In Progress
State
In Review
State
Paused
State
Unverified
State
Verified
State
Wont Do
Type
Automation
Type
Bug
Type
Discussion
Type
Documentation
Type
Epic
Type
Feature
Type
Legendary
Type
Refactor
Type
Support
Type
Task
Type
Testing
Milestone
Clear milestone
No items
No milestone
v3.6.0
Projects
Clear projects
No items
No project
Assignees
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1 participant
Notifications
Due date
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Blocks
#1020 [Epic] Database resource hierarchy restructuring
cleveragents/cleveragents-core
Reference
cleveragents/cleveragents-core#2418
No description provided.