How to Resume Interrupted ARS Pipeline Sessions Using the Material Passport

The Material Passport acts as a persistent, append-only ledger that enables users to resume interrupted ARS pipeline sessions by emitting cryptographic reset boundaries and validating them via resume_from_passport=<hash> in a fresh Claude Code session.

The Academic Research Skills (ARS) suite orchestrates multi-agent research workflows inside Claude Code containers that are isolated by design—state does not survive across browser tabs or new sessions. To resume interrupted ARS pipeline sessions without losing progress or provenance, the system leverages the Material Passport (Schema 9) as a single source of truth. This append-only ledger records every handoff artifact together with integrity metadata, enabling a reset-boundary mechanism that restores execution from the exact point of interruption.

Understanding Session Isolation and the Material Passport

Claude Code runs each conversation in an ephemeral container, meaning variables, memory, and intermediate files vanish when the session ends. The Material Passport solves this by functioning as an externalized state machine defined in shared/handoff_schemas.md under Schema 9.

Rather than storing session data in volatile memory, the passport persists as a YAML artifact that accompanies your project. It tracks:

• Provenance chains for every generated artifact
• Version labels and integrity timestamps
• Reset boundaries that demarcate resumable checkpoints

Because the passport is append-only, it maintains an immutable audit trail even when the pipeline pauses or crashes.

The Reset-Boundary Mechanism (v3.6.3)

Introduced in version v3.6.3, the reset-boundary feature allows the pipeline to emit durable checkpoints when the environment variable ARS_PASSPORT_RESET=1 is set. When a FULL checkpoint completes, the orchestrator automatically appends a boundary entry to the passport’s reset_boundary[] ledger.

According to shared/contracts/passport/reset_ledger_entry.schema.json, each boundary entry contains:

• A cryptographic hash of the checkpoint state
• The completed stage number and next stage pointer
• Session markers and generation timestamps
• Optional pending-decision metadata

The full contract for this behavior is documented in academic-pipeline/references/passport_as_reset_boundary.md.

Step 1: Emitting a Boundary Entry

To create a resumable checkpoint, ensure ARS_PASSPORT_RESET=1 is exported before running a stage that produces a FULL artifact. The resulting passport snippet will resemble the following structure:

# Example Material Passport snippet (generated after a FULL checkpoint)

# File: passport.yaml

reset_boundary:
  - kind: boundary
    hash: a3f2b7c9d0e1
    stage: "2"
    next: "2.5"
    generated_at: 2026-04-23T14:00:00Z
    session_marker: sess-20260423-1a2b
    version_label: paper_draft_v1
    mode: full
    verification_status: VERIFIED

The hash field (a 12-character hexadecimal string) serves as the canonical pointer to this specific state. The orchestrator writes this entry atomically to prevent corruption during sudden session termination.

Step 2: Resuming with resume_from_passport

When you open a fresh Claude Code session, paste the resume command followed by the boundary hash. The orchestrator—implemented in academic-pipeline/agents/pipeline_orchestrator_agent.md under the Resume Mode section—parses this directive to reconstruct the pipeline state.

Basic resumption syntax:

resume_from_passport=a3f2b7c9d0e1

You may override the target stage or execution mode by appending parameters:

resume_from_passport=a3f2b7c9d0e1 stage=5 mode=revision

Upon receiving this command, the orchestrator:

1. Validates the hash against the reset_boundary[] ledger in the provided passport
2. Appends a resume entry that points to the consumed boundary (maintaining the audit trail)
3. Verifies that the verification_status and timestamp meet freshness requirements
4. Re-executes integrity checks only on artifacts that have been modified since the boundary was written

Integrity Verification and Audit Artifacts

Resuming is not merely a matter of loading state; the orchestrator must ensure that no files have been tampered with externally. As of v3.6.7, the passport supports an audit_artifact[] array that records Layer-2 and Layer-3 verification results.

When you resume interrupted ARS pipeline sessions, scripts/check_audit_artifact_consistency.py re-runs eleven distinct audit checks against any persisted artifacts. If a file’s hash differs from the recorded value, the script marks the entry as STALE, forcing the pipeline to re-verify that artifact through the full integrity gate (Stage 2.5) before proceeding.

This re-verification step prevents silent data corruption and ensures that the provenance chain remains intact across disjointed sessions.

Version Tracking and Freshness Rules

To skip redundant stages safely, the Material Passport must satisfy three conditions defined in shared/handoff_schemas.md under Validation Rules:

• verification_status must equal VERIFIED
• integrity_pass_date must be less than 24 hours old
• version_label must match the current artifact being processed

If any condition fails—for example, if the passport is older than 24 hours—the orchestrator discards the shortcut and re-executes the full integrity gate. This time-bound validation ensures that stale checkpoints do not propagate outdated assumptions into new research sessions.

Summary

• The Material Passport (Schema 9) provides an append-only ledger that persists ARS pipeline state across ephemeral Claude Code sessions.
• Set ARS_PASSPORT_RESET=1 to emit boundary entries containing cryptographic hashes at every FULL checkpoint.
• Resume by supplying resume_from_passport=<hash> in a new session; the orchestrator validates the hash, appends a resume entry, and restores execution from the recorded stage.
• Re-verification via check_audit_artifact_consistency.py ensures that altered artifacts are marked STALE and re-checked before the pipeline continues.
• Freshness rules (24-hour window, VERIFIED status, matching version labels) govern whether stages can be skipped or must be re-executed.

Frequently Asked Questions

What happens if I modify files after creating a boundary but before resuming?

If you modify any tracked files, the re-verification step will detect the discrepancy when check_audit_artifact_consistency.py compares the current filesystem state against the audit_artifact[] ledger. The affected artifacts will be marked STALE, and the orchestrator will require you to re-run the integrity gate (Stage 2.5) before advancing to subsequent stages. This prevents corrupted or inconsistent states from propagating through the resumed session.

Can I resume a session on a different machine or browser?

Yes. Because the Material Passport is a portable YAML file rather than local memory, you can copy the passport and the associated project files to any environment with Claude Code installed. As long as the passport contains a valid boundary entry and you provide the correct hash via resume_from_passport, the orchestrator will restore the pipeline state identically, regardless of the original session’s container.

How long does a boundary entry remain valid for resumption?

Boundary entries are valid for 24 hours from the timestamp recorded in integrity_pass_date. After this window expires, the freshness rules in handoff_schemas.md force the orchestrator to invalidate the shortcut and re-execute the full integrity verification. You can generate a new boundary at any time by re-running a FULL checkpoint with ARS_PASSPORT_RESET=1 set.

What is the difference between a boundary entry and a resume entry?

A boundary entry is written when the pipeline reaches a checkpoint (kind: boundary) and represents a stable state from which future sessions can start. A resume entry (kind: resume) is appended when you actually invoke resume_from_passport in a new session, creating an audit trail that links the new execution context to the specific boundary being consumed. This dual-entry system maintains an immutable provenance chain showing exactly when and how the pipeline was interrupted and restarted.

{
  "mcpServers": {
    "instagit": {
      "command": "npx",
      "args": ["-y", "instagit@latest"]
    }
  }
}