Session Management

This skill enacts the Algorithms Before Tokens axiom from MANIFESTO.md by encoding the full session lifecycle as a deterministic procedure. Session management is governed by AGENTS.md § Agent Communication — every rule in this skill derives from that section. Read AGENTS.md before deviating from any step below.

1. File Structure

The scratchpad lives in .tmp/ at the workspace root. It is gitignored and never committed.

.tmp/
  <branch-slug>/          # branch name with / replaced by -
    _index.md             # one-line stubs of all closed sessions on this branch
    <YYYY-MM-DD>.md       # one file per session day — the active scratchpad

<branch-slug> examples:

• Branch main → .tmp/main/
• Branch feat/agent-skills → .tmp/feat-agent-skills/
• Branch docs/update-guides → .tmp/docs-update-guides/

The _index.md accumulates single-line stubs for every closed session on the branch. Future sessions read it for fast orientation without opening old files.

2. Session Start

Context Snapshot Before Reset

Before calling prune_scratchpad.py --init during error recovery, save a snapshot of the current context:

uv run python scripts/prune_scratchpad.py --snapshot

This saves .tmp/<branch>/<date>-snapshot.yaml containing: task_name, task_parameters, timestamp, and active scratchpad section.

After re-entry into the failed task's decision point, compare contexts:

uv run python scripts/compare_context_snapshot.py \
  --snapshot ".tmp/$(git branch --show-current | tr '/' '-')/$(date +%Y-%m-%d)-snapshot.yaml"

If equivalent: true → do not re-attempt. Escalate to user: "My context is identical to the failed attempt. New direction needed."

Encoding point: Research basis: docs/research/orchestrator-autopilot-failure.md § Recommendation 5. Scripts: scripts/prune_scratchpad.py --snapshot, scripts/compare_context_snapshot.py.

2.1 Initialize the Scratchpad

At the beginning of every session, run:

uv run python scripts/prune_scratchpad.py --init

This creates .tmp/<branch-slug>/<today>.md if it does not exist. If the file already exists (resuming a session mid-day), it is unchanged.

Start the scratchpad watcher in a background terminal:

uv run python scripts/watch_scratchpad.py

The watcher auto-annotates every H2 heading with its current line range (## My Section [L12–L47]), enabling precise line-number references in agent delegations.

2.2 Session-Start Encoding Checkpoint

Requirement: The very first sentence written in ## Session Start must name the governing axiom and one primary endogenous source — before any tool calls, file reads, or task execution.

Format:

## Session Start

**Session-Start Checkpoint**: This session is governed by Axiom N (Name).
Primary endogenous source: `<path>` — <one sentence on why this source is consulted first>.

Examples by session type:

• Research session: "This session is governed by Axiom 1 (Endogenous-First). Primary endogenous source: docs/research/OPEN_RESEARCH.md — frames the research question before any web fetching."
• Scripting session: "This session is governed by Axiom 2 (Algorithms Before Tokens). Primary endogenous source: scripts/watch_scratchpad.py — canonical example of automating a repeated manual task."
• Documentation session: "This session is governed by Axiom 1 (Endogenous-First). Primary endogenous source: docs/guides/workflows.md — existing patterns to extend rather than re-author."

Why this matters: Low checkpoint-density in scratchpad history is a leading indicator of encoding drift. Auditors can verify whether the stated axiom is consistent with the actions taken. If it is not, the session has drifted from the governing constraint in AGENTS.md.

2.3 Read Before Acting

If this is a continuation session (an open branch with prior scratchpad entries), read the _index.md and today's scratchpad file before delegating:

# Orientation read — always do this before Phase 1
read_file .tmp/<branch-slug>/_index.md
read_file .tmp/<branch-slug>/<today>.md

If there is a workplan (docs/plans/<date>-<slug>.md), read it as well. The workplan is the plan of record; the scratchpad is the live inter-agent memory.

2.4 MCP Health Check

After the scratchpad is initialised, call check_substrate via the MCP server to confirm the repo is in a valid state before any phase begins:

check_substrate()

Log the result summary under ## Session Start in the scratchpad. A red result is a blocking issue — fix the reported violation before delegating any phase. A green result is sufficient to proceed.

Preferred substitution: if the MCP server is connected, use prune_scratchpad(dry_run=true) in place of the cat .tmp/... orientation read in §2.3 — it returns the current scratchpad state as structured output without requiring a separate terminal command.

If the MCP server is not connected (e.g. CI or non-VS Code environment), run the equivalent directly:

uv run python scripts/check_substrate_health.py

3.0 Interrupt Check (Pre-Phase Gate)

Before every phase action and before executing any tool call, check whether the user's most recent message contains an interruption signal (STOP, DO NOT CONTINUE, ABORT, ABORT THIS TASK, CANCEL, PAUSE EXECUTION, HOLD).

If interrupted:

1. Write to scratchpad: ## Interrupted: [current task name] — awaiting user direction
2. Commit any in-progress file changes: git add -A && git commit -m "chore: checkpoint before interrupt — [task]"
3. Return to user: "Execution paused at [phase name]. What would you like to do next?"
4. Do NOT proceed with the next planned step.

MCP tool (when server connected): detect_user_interrupt() — returns true if the last user message contains interrupt keywords. Wire into pre-phase sequence.

Cross-reference: AGENTS.md § Instruction Hierarchy for the full hierarchy and keyword list.

3. Phase Gate Protocol

3.1 Phase Output Headings

Each delegated agent appends findings under its own named section:

## <AgentName> Output

<findings here>

Standard headings: ## Scout Output, ## Synthesizer Output, ## Reviewer Output, ## Archivist Output, ## Executive Output.

Section-scope isolation rule: each agent writes only to its own heading and reads only its own prior section. The Executive is the sole integration point — it alone reads the full scratchpad across all agents. Subagents never read laterally across other sections.

3.2 Handoff Notes

When handing off to another agent, write a structured note:

## Handoff to <Next Agent>

- **Completed**: <what was done>
- **Next steps**: <what the receiving agent should do>
- **Files changed**: <list>
- **Open questions**: <anything unresolved>

3.3 Escalation Notes

When a subagent cannot complete a task:

## <AgentName> Escalation

- **Current state**: <what was completed>
- **Blocking issue**: <what requires elevated posture>
- **Recommended action**: <which agent to invoke>
- **Instructions**: <step-by-step for the receiving agent>

3.4 Workplan Phase Status

Update phase status markers in docs/plans/<date>-<slug>.md as phases complete. Use ✅ for done, ⬜ for pending. Commit the workplan after each phase marks complete — the workplan is a committed, auditable record, not ephemeral context.

4. Compaction Guard

VS Code Copilot Chat may compact conversation history at any time — automatically (context window full) or manually via /compact. Compaction replaces detailed history with a <conversation-summary> block. The scratchpad survives compaction. The conversation history does not.

4.1 Pre-Compact Checkpoint Sequence

When the context window is above 75%, or before running /compact manually:

1. Write a ## Pre-Compact Checkpoint section to the scratchpad:

   ## Pre-Compact Checkpoint
   
   - **Current state**: <what has been done so far>
   - **Next action**: <the single next step after compaction>
   - **Open questions**: <anything unresolved>
   - **Files in flight**: <uncommitted changes, if any>

2. Commit all in-progress file changes:

   git add -A && git commit -m "chore: pre-compact checkpoint"

3. Update the workplan — tick completed phases.

4. Optionally prune the scratchpad to keep the post-compact re-read fast:

   uv run python scripts/prune_scratchpad.py --dry-run   # check first
   uv run python scripts/prune_scratchpad.py

5. Run /compact in VS Code Copilot Chat.

4.2 Post-Compact Recovery

After compaction, the <conversation-summary> block is the only conversation context. Immediately re-orient from disk:

1. Re-read the scratchpad: read_file .tmp/<branch-slug>/<today>.md
2. Re-read the workplan: read_file docs/plans/<current-plan>.md
3. Run git status — confirm what is committed vs. in-flight
4. Do not assume the compaction summary captured everything. Trust files on disk, not the summary.

4.3 Compaction-Safe Writing Habits

Rule: treat every important finding as if the next token will trigger compaction. If it is not in the scratchpad, it is lost.

5. Batch Subagent Handoffs

When a session involves multiple parallel subagents (e.g., multiple Research Scouts), use JSONL (JSON Lines) as the canonical format for batch handoffs and streamed context.

Schema convention for Scout output objects:

{"agent": "str", "source": "str", "confidence": "float", "finding": "str"}

Source: docs/research/agent-fleet-model-diversity-and-structured-formats.md (§ Recommendations 3).

JSONL preservation ensures that append-only write semantics are maintained across isolated subagent context windows without requiring atomic file locks.

6. Size Management

Pruning compresses "archived" sections (headings containing: Results, Output, Done, Completed, Summary, Handoff) to single-line stubs, and preserves "live" sections (containing: Active, Plan, Session, Escalation) in full. It appends a one-line stub to _index.md on --force.

Always dry-run before pruning:

uv run python scripts/prune_scratchpad.py --dry-run

5.1 Tracked Workplans (docs/plans/)

For any multi-phase session (≥ 3 phases or ≥ 2 agent delegations, or spanning more than one day), create a workplan before execution begins and commit it to docs/plans/. Governed by AGENTS.md § Agent Communication — Programmatic-First applied to session planning.

Naming: docs/plans/YYYY-MM-DD-<brief-slug>.md (date-first for chronological sorting)

Required contents:

• Objective
• Phase plan: agent, deliverables, depends-on, status — with a Review gate phase after every domain phase
• Acceptance criteria checklist

Use docs/plans/2026-03-06-formalize-workflows.md as the canonical template.

Commit the workplan at the start of the session (before Phase 1 executes), then update status markers (⬜ Not started, ⏳ In progress, ✅ Complete) as phases complete. See § 3.4 for the phase status update pattern.

Fleet coherence mechanism: a committed workplan gives every downstream execution agent (Scout, Synthesizer, Reviewer) a shared written specification to verify against — without the Orchestrator re-explaining scope at each handoff. Coherence emerges from the artifact, not from the Orchestrator's presence at every step.

5.2 Per-Phase Execution Checklists

Before delegating any multi-step execution phase, the Orchestrator delegates a detailed per-phase checklist to the Executive Planner first. The Planner's checklist functions as a shared coherence artifact: every downstream execution agent independently verifies their output against it, eliminating interpretive drift without requiring the Orchestrator to re-explain scope mid-phase.

Flow:

• Workplan created → delegate checklist creation to Executive Planner
• Checklist committed to scratchpad or workplan doc before Phase 1 begins
• Each execution phase invocation references the checklist as its acceptance criteria

Hard gate (≥3 phases or ≥2 delegations): The Executive Planner must produce per-phase checklists before the first domain phase delegation begins. This is not optional. Skipping this step produces a ~1 audit-round overhead to recover mid-phase scope gaps — observed twice in the 2026-03-13 Dogma Update Sprint (Phase 5 recast, Phase 1A sub-issue gap). Write "Planner checklist received" in the scratchpad before delegating Phase 1.

Audit Trail

Every irreversible or external-state-modifying action taken during a session must be recorded under a ## Audit Trail heading in the scratchpad.

Required fields per entry

Example entry

- timestamp: "2026-03-26T14:32:00Z"
  action: "gh issue comment 333 --body-file /tmp/note.md"
  agent: "Executive Orchestrator"
  outcome: "success"

Write an Audit Trail entry immediately after any git push, gh issue create/comment/close, gh pr create, or bulk file operation affecting committed state.

Telemetry

For each agent invocation that produces a measurable span, record OTel metadata under a ## Telemetry heading in the scratchpad. Entry shape is consistent with ## Audit Trail — one YAML block per invocation.

Required sub-fields per entry

Example entry

- span_id: "3a2b1c4d5e6f"
  model: "claude-sonnet-4"
  input_tokens: 4200
  output_tokens: 612
  latency_ms: 3840

Values come from gen_ai.* OTel attributes — see docs/research/otel-agent-instrumentation.md Pattern 2 for the canonical attribute names and Pattern 1 for the span shape.

6. Session Close

6.1 Session Summary

The executive agent writes a ## Session Summary section to the scratchpad:

## Session Summary

**Branch**: <branch-slug>
**Date**: <YYYY-MM-DD>
**Phases completed**: <list>
**Key decisions**: <bullet list>
**Files committed**: <list>
**Recommended next session**: <one sentence>

6.2 Issue Progress Comments

Post a progress comment on every GitHub issue actively worked during the session. Write the body to a temp file — never use --body "..." with multi-line content:

# Validate temp file before consumption
test -s /tmp/session_close_<num>.md || { echo "ERROR: temp file empty"; exit 1; }
file /tmp/session_close_<num>.md | grep -q "UTF-8\|ASCII" || { 
  echo "ERROR: file not valid UTF-8"; exit 1; 
}

# Safe to use
gh issue comment <num> --body-file /tmp/session_close_<num>.md

# Verify the comment landed:
gh issue view <num> --json comments -q '.comments[-1].body[:80]'

6.3 Issue Checkbox Updates

Update the issue body checkboxes to reflect completed deliverables:

# Validate temp file before consumption
test -s /tmp/issue_<num>_body.md || { echo "ERROR: temp file empty"; exit 1; }
file /tmp/issue_<num>_body.md | grep -q "UTF-8\|ASCII" || { 
  echo "ERROR: file not valid UTF-8"; exit 1; 
}
grep -q "- \[.\]" /tmp/issue_<num>_body.md || { 
  echo "WARNING: no checkbox patterns found"; 
}

# Safe to use
gh issue edit <num> --body-file /tmp/issue_<num>_body.md

# Verify
gh issue view <num> --json body -q '.body' | grep -E '\[x\]|\[ \]'

6.4 PR Review Triage (If a PR Is Open)

This step must run before any session that opens a PR or works on a branch with an open PR.

A PR is not ready to merge until all automated reviews are triaged. Copilot review is triggered automatically when a PR is opened — it must be handled before the session closes with "PR is open — ready to merge."

# Check PR state and any reviews
gh pr view --json number,state,reviews,reviewThreads 2>/dev/null && \
  gh api repos/<owner>/<repo>/pulls/<num>/comments \
    --jq '.[] | {id, path, body}'

For each review:

1. Classify every comment as Blocking / Suggestion / Nit / Question
2. Fix all Blocking items and commit
3. Post batch replies via scripts/pr_review_reply.py
4. Resolve all addressed threads
5. Re-request review if state was CHANGES_REQUESTED

See the pr-review-triage skill for the full workflow.

Anti-pattern: Ending a session with "PR is open — merge when ready" without running this check. This is a hard encoding violation regardless of CI status.

6.5 Archive and Stop

uv run python scripts/prune_scratchpad.py --force
# Stop the scratchpad watcher (Ctrl-C in its terminal)

7. Quick Reference

# Initialize today's session file
uv run python scripts/prune_scratchpad.py --init

# Start auto-annotator (keep running in background)
uv run python scripts/watch_scratchpad.py

# Dry-run prune (check what will be compressed)
uv run python scripts/prune_scratchpad.py --dry-run

# Prune in-place (when file exceeds 2000 lines)
uv run python scripts/prune_scratchpad.py

# Force prune + archive session (at session end)
uv run python scripts/prune_scratchpad.py --force

8. Governing Constraint

This skill is governed by AGENTS.md § Agent Communication. All rules in this skill are re-encodings of that section. When AGENTS.md and this skill conflict, AGENTS.md takes precedence. The encoding inheritance chain is:

MANIFESTO.md → AGENTS.md → agent files → this skill → session behaviour.

Cross-reference density (back-references to MANIFESTO.md or AGENTS.md in session output) is a proxy for encoding fidelity. Low density signals likely drift.