indexer-agent reconciliation loop overrides manual graphman pause

Summary

When using graphman pause <deployment> to manually pause a subgraph, the indexer-agent's reconcileDeployments loop automatically resumes it within minutes by calling subgraph_deploy on the graph-node JSON-RPC admin API. This makes it impossible to keep a subgraph paused for maintenance operations such as graphman rewind.

Steps to reproduce

1. graphman pause <IPFS_HASH>
2. Wait 2-5 minutes (one reconciliation cycle)
3. graphman info <IPFS_HASH> --status → shows Paused: false

The subgraph has decisionBasis: always in indexer rules.

Expected behavior

The reconciliation loop should check the paused_at field before calling subgraph_deploy. If a deployment was explicitly paused via graphman, the agent should not resume it.

Impact

• Cannot perform graphman rewind safely — the subgraph resumes indexing during the rewind, causing data inconsistencies
• Any maintenance operation requiring a temporary stop is compromised
• Operators must resort to workarounds like reassigning to a non-existent node (e.g. graphman reassign <hash> maintenance_node_0) to prevent the agent from resuming the subgraph

Root cause

In packages/indexer-agent/src/agent.ts, the reconcileDeployments function calculates target deployments based on indexer rules and calls this.graphNode.ensure() for each one. There is no check for whether a deployment is currently paused before calling ensure. If the deployment is in the target list (active allocation or decisionBasis: always/offchain), it will be re-deployed, which implicitly resumes it.

Suggested fix

Before calling ensure for a deployment, check if it is currently paused (paused_at IS NOT NULL). If paused, skip the ensure call. Optionally, add a --force flag to graphman pause or a new indexer rule field (e.g. maintenancePause: true) that the agent explicitly respects.

Related issues

• #713 — Added --deployment-management manual mode as a workaround (disables entire reconciliation loop)
• #853 — Aimed to make the agent respect the new pause mechanism, but the "use new pausing mechanism" task was never completed
• graphprotocol/graph-node#4255 — Introduced first-class graphman pause/resume commands
• graphprotocol/graph-node#5253 — graphman reassign should pause the subgraph first (still OPEN)
• graphprotocol/graph-node#5110 — graphman rewind should use the pause mechanism (closed by stale bot, never implemented)

Current workaround

Reassign the subgraph to a non-existent node before maintenance:

graphman pause <IPFS_HASH>
graphman reassign <IPFS_HASH> maintenance_node_0
# perform maintenance (rewind, reindex, etc.)
graphman reassign <IPFS_HASH> index_node_0
graphman resume <IPFS_HASH>

The indexer-agent cannot resume the subgraph because maintenance_node_0 does not exist.

Start in packages/indexer-agent/src/agent.ts at reconcileDeployments and trace how target deployments reach this.graphNode.ensure(). Check how the paused_at field is exposed and reproduce the graphman pause scenario; done means an explicitly paused deployment is not resumed during reconciliation while normal deployments still reconcile.