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When a Continuity agent starts a session, it does not simply read a config file and begin work. It runs a structured reconstitution procedure that rebuilds its full operational state from durable artifacts — checking the environment, loading files in order, reconciling parent-child relationships, validating required fields, and declaring a status before taking any action. This page explains that procedure in full.

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Two boot scenarios

Continuity handles two distinct situations at boot time, and the procedure is the same for both. New agent from templates: Copy the template files, replace {{PLACEHOLDER}} values with your agent’s real identity, and run INIT.md. The procedure creates AGENTS.md if it does not exist, loads all files in the declared order, and declares READY when everything checks out. Existing agent assimilating: An agent that already has scattered state files — ad-hoc instructions, memory in various formats, identity spread across multiple documents — runs INIT.md against its current workspace. The procedure inspects what exists, maps that state onto the Continuity file structure, creates missing files, and reconciles. Existing agents do not need to start from scratch.

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The 9-stage INIT procedure

INIT.md is the reconstitution procedure. Run it on every session start to rebuild operational state from durable artifacts. 
PREFLIGHT → INSPECT → SCAN → LOAD → RECONCILE → DISCOVER → VALIDATE → DECLARE → SNAPSHOT
1

PREFLIGHT

Confirm the host environment before touching any state files.
  • Confirm host environment: container, OS, timezone, locale
  • Confirm user identity and authority context
  • Confirm network egress/ingress and available endpoints
If the environment is incoherent at this stage, the agent stops and reports. It does not proceed to INSPECT with an unknown environment.
2

INSPECT

Examine the workspace for required files and available resources.
  • List root files and confirm presence of canonical files (per the load order in AGENTS.md)
  • Check disk space — if usage exceeds 90%, declare BLOCKED
  • Check memory pressure and inode usage
INSPECT is a non-destructive read: it observes but does not create or modify anything.
3

SCAN

Discover the file hierarchy and screen for security threats.
  • Recursively scan subdirectories for local AGENTS.md files
  • Build the hierarchy tree: identify parent/child relationships and record the parent path for each AGENTS.md found
  • Scan context files for prompt injection markers, hidden HTML/JS, credential exfiltration patterns, and invisible characters
  • Quarantine failures in logs/quarantine/
The security scan runs here, before any files are loaded, so that malicious content cannot influence the reconstitution procedure itself.
4

LOAD

Read all files in the declared load order.
  • Read all files in the load order defined in AGENTS.md
  • Read SNAPSHOT.md (last known good state)
  • Read LEARNINGS.md (insights and soft rules from prior sessions)
Files are loaded in the specific order declared in AGENTS.md — identity files first, then capability files, then operational state, then task and planning files. Load order matters because later files may reference state established by earlier ones.
5

RECONCILE

Resolve the parent/child hierarchy and identify any state drift.
  • Load parent AGENTS.md before child; reconcile each level of the hierarchy
  • Compare STATE.md with SNAPSHOT.md — identify drift between last known good state and current state
  • Compare CONTEXT.md with the current environment — identify changes since last session
  • Compare parent authority with local AGENTS.md — a child may refine scope but may not weaken parent constraints
  • If contradictions exist, parent wins; add to STATE.md blockers
Reconciliation is how the agent detects that something changed between sessions — a task that was in progress is now blocked, an infrastructure endpoint is unreachable, a parent constraint has been updated.
6

DISCOVER

Load available tools and discover connected services.
  • Load available tools from the agent framework
  • If .mcp.json is present, discover MCP servers
  • If agents.json is present, load bound agent profiles
  • List loaded skills
  • Record partner endpoints but do not block on reachability
Discovery is optimistic: the agent records what it finds but does not fail if an endpoint is temporarily unreachable. Reachability failures become warnings, not blockers.
7

VALIDATE

Check that all required files exist, are structurally valid, and contain the expected fields.The validation table covers every required file:
FileMust have
AGENTS.mdExists and is valid
IDENTITY.mdExists and is valid
SELF.mdDefines operating principles and non-goals
SOUL.mdDefines essence and purpose
STATE.mdDefines status, active_objective, next_valid_action
CONTEXT.mdExists and is valid
INIT.mdExists and is valid
TODO.mdExists and is valid
PLAN.mdExists and is valid
TOOLS.mdExists and is valid
SNAPSHOT.mdTimestamp within last 7 days (else READY_WITH_WARNINGS)
Each row is a checkbox — all must be checked before DECLARE can issue READY.
8

DECLARE

Issue the boot status and write it into STATE.md.The possible outcomes:
  • READY — all files present, no blockers, no warnings
  • READY_WITH_WARNINGS — operational but with caveats (stale snapshot, unreachable partner, optional file missing)
  • BLOCKED — missing required file or critical blocker; the agent must not proceed
The declaration is written into STATE.md and appended to logs/events.jsonl:
Status: [READY / READY_WITH_WARNINGS / BLOCKED]
Warnings: [LIST_OR_NONE]
Blockers: [LIST_OR_NONE]
Objective: [FROM_PLAN_MD]
9

SNAPSHOT

If initialization changed any state, refresh the restoration anchor.
  • If initialization changed state, refresh SNAPSHOT.md
  • Write an immutable copy to snapshots/YYYY-MM-DDTHH-MM-SS.md
This ensures that the next boot has an accurate restoration anchor, even if the session ends unexpectedly before the agent gets to do any work.
FileWhenWhat
INIT.mdFirst run + every session startReconstitution procedure. 9 stages. Creates AGENTS.md if missing.
AGENTS.mdEvery sessionLiving instruction file. Bootloader + runtime parameters + project guard.
BOOT.mdEvery wake (optional)Lightweight CHECK → ACT → REPORT cycle for heartbeats between full reconstitutions.
BOOTSTRAP.mdFirst run onlyIdentity discovery ritual. Guides the very first session. Self-destructing after use.
BOOT.md is not a replacement for INIT.md. INIT runs the full 9-stage reconstitution and is required at session start. BOOT is a lightweight alternative for agents that wake on a schedule — it reads STATE.md, checks TODO.md, acts if there’s work to do, and updates CONTEXT.md. If the agent is confused about state, stop using BOOT and run INIT instead.

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Post-boot states

After DECLARE runs, the agent’s status is one of three values:
All required files are present and valid. No blockers. No warnings. The snapshot is fresh (within 7 days). The agent can proceed immediately to its active objective.
Status: READY
Warnings: NONE
Blockers: NONE
Objective: [from PLAN.md]

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Existing agents: mapping state onto the file structure

An existing agent — one with scattered notes, ad-hoc instructions, or memory in a custom format — assimilates into Continuity by running INIT.md against its current workspace. The procedure does not require a blank slate. INIT.md’s INSPECT and SCAN stages identify what already exists. RECONCILE maps it onto the file structure: existing notes become MEMORY.md entries, current instructions become the body of AGENTS.md, task lists become TODO.md. Missing files are created from templates with {{PLACEHOLDER}} values left for the operator to fill in. The result is a workspace that has a valid Continuity structure even if it started as something else entirely.
After assimilation, run the post-boot checklist from USAGE.md: confirm all {{PLACEHOLDER}} values are replaced, verify STATE.md declares a status, ensure secrets are in .secrets/ or environment variables rather than in markdown files, and delete BOOTSTRAP.md once identity is established.

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