---
summary: "Deep dive: session store + transcripts, lifecycle, and (auto)compaction internals"
read_when:
  - You need to debug session ids, transcript JSONL, or sessions.json fields
  - You are changing auto-compaction behavior or adding "pre-compaction" housekeeping
  - You want to implement memory flushes or silent system turns
title: "Session management deep dive"
---

Nodmix manages sessions end-to-end across these areas:

- **Session routing** (how inbound messages map to a `sessionKey`)
- **Session store** (`sessions.json`) and what it tracks
- **Transcript persistence** (`*.jsonl`) and its structure
- **Transcript hygiene** (provider-specific fixups before runs)
- **Context limits** (context window vs tracked tokens)
- **Compaction** (manual and auto-compaction) and where to hook pre-compaction work
- **Silent housekeeping** (memory writes that should not produce user-visible output)

If you want a higher-level overview first, start with:

- [Session management](/concepts/session)
- [Compaction](/concepts/compaction)
- [Memory overview](/concepts/memory)
- [Memory search](/concepts/memory-search)
- [Session pruning](/concepts/session-pruning)
- [Transcript hygiene](/reference/transcript-hygiene)

---

## Source of truth: the Gateway

Nodmix is designed around a single **Gateway process** that owns session state.

- UIs (macOS app, web Control UI, TUI) should query the Gateway for session lists and token counts.
- In remote mode, session files are on the remote host; "checking your local Mac files" won't reflect what the Gateway is using.

---

## Two persistence layers

Nodmix persists sessions in two layers:

1. **Session store (`sessions.json`)**
   - Key/value map: `sessionKey -> SessionEntry`
   - Small, mutable, safe to edit (or delete entries)
   - Tracks session metadata (current session id, last activity, toggles, token counters, etc.)

2. **Transcript (`<sessionId>.jsonl`)**
   - Append-only transcript with tree structure (entries have `id` + `parentId`)
   - Stores the actual conversation + tool calls + compaction summaries
   - Used to rebuild the model context for future turns
   - Compaction checkpoints are metadata over the compacted successor
     transcript. New compactions do not write a second `.checkpoint.*.jsonl`
     copy.

Gateway history readers should avoid materializing the whole transcript unless
the surface explicitly needs arbitrary historical access. First-page history,
embedded chat history, restart recovery, and token/usage checks use bounded tail
reads. Full transcript scans go through the async transcript index, which is
cached by file path plus `mtimeMs`/`size` and shared across concurrent readers.

---

## On-disk locations

Per agent, on the Gateway host:

- Store: `~/.nodmix/agents/<agentId>/sessions/sessions.json`
- Transcripts: `~/.nodmix/agents/<agentId>/sessions/<sessionId>.jsonl`
  - Telegram topic sessions: `.../<sessionId>-topic-<threadId>.jsonl`

Nodmix resolves these via `src/config/sessions.ts`.

---

## Store maintenance and disk controls

Session persistence has automatic maintenance controls (`session.maintenance`) for `sessions.json`, transcript artifacts, and trajectory sidecars:

- `mode`: `warn` (default) or `enforce`
- `pruneAfter`: stale-entry age cutoff (default `30d`)
- `maxEntries`: cap entries in `sessions.json` (default `500`)
- `resetArchiveRetention`: retention for `*.reset.<timestamp>` transcript archives (default: same as `pruneAfter`; `false` disables cleanup)
- `maxDiskBytes`: optional sessions-directory budget
- `highWaterBytes`: optional target after cleanup (default `80%` of `maxDiskBytes`)

Normal Gateway writes flow through a per-store session writer that serializes in-process mutations without taking a runtime file lock. Hot-path patch helpers borrow the validated mutable cache while they hold that writer slot, so large `sessions.json` files are not cloned or reread for every metadata update. Runtime code should prefer `updateSessionStore(...)` or `updateSessionStoreEntry(...)`; direct whole-store saves are compatibility and offline-maintenance tools. When a Gateway is reachable, non-dry-run `nodmix sessions cleanup` and `nodmix agents delete` delegate store mutations to the Gateway so cleanup joins the same writer queue; `--store <path>` is the explicit offline repair path for direct file maintenance. `maxEntries` cleanup is still batched for production-sized caps, so a store may briefly exceed the configured cap before the next high-water cleanup rewrites it back down. Session store reads do not prune or cap entries during Gateway startup; use writes or `nodmix sessions cleanup --enforce` for cleanup. `nodmix sessions cleanup --enforce` still applies the configured cap immediately and prunes old unreferenced transcript, checkpoint, and trajectory artifacts even when no disk budget is configured.

Maintenance keeps durable external conversation pointers such as group sessions
and thread-scoped chat sessions, but synthetic runtime entries for cron, hooks,
heartbeat, ACP, and sub-agents can still be removed when they exceed the
configured age, count, or disk budget.

Nodmix no longer creates automatic `sessions.json.bak.*` rotation backups during Gateway writes. The legacy `session.maintenance.rotateBytes` key is ignored and `nodmix doctor --fix` removes it from older configs.

Transcript mutations use a session write lock on the transcript file. Lock acquisition waits up to
`session.writeLock.acquireTimeoutMs` before surfacing a busy-session error; the default is `60000`
ms. Raise this only when legitimate prep, cleanup, compaction, or transcript mirror work contends
longer on slow machines. `session.writeLock.staleMs` controls when an existing lock can be
reclaimed as stale; the default is `1800000` ms. `session.writeLock.maxHoldMs` controls the
in-process watchdog release threshold; the default is `300000` ms. Emergency env overrides are
`NODMIX_SESSION_WRITE_LOCK_ACQUIRE_TIMEOUT_MS`, `NODMIX_SESSION_WRITE_LOCK_STALE_MS`, and
`NODMIX_SESSION_WRITE_LOCK_MAX_HOLD_MS`.

Enforcement order for disk budget cleanup (`mode: "enforce"`):

1. Remove oldest archived, orphan transcript, or orphan trajectory artifacts first.
2. If still above the target, evict oldest session entries and their transcript/trajectory files.
3. Keep going until usage is at or below `highWaterBytes`.

In `mode: "warn"`, Nodmix reports potential evictions but does not mutate the store/files.

Run maintenance on demand:

```bash
nodmix sessions cleanup --dry-run
nodmix sessions cleanup --enforce
```

---

## Cron sessions and run logs

Isolated cron runs also create session entries/transcripts, and they have dedicated retention controls:

- `cron.sessionRetention` (default `24h`) prunes old isolated cron run sessions from the session store (`false` disables).
- `cron.runLog.maxBytes` + `cron.runLog.keepLines` prune `~/.nodmix/cron/runs/<jobId>.jsonl` files (defaults: `2_000_000` bytes and `2000` lines).

When cron force-creates a new isolated run session, it sanitizes the previous
`cron:<jobId>` session entry before writing the new row. It carries safe
preferences such as thinking/fast/verbose settings, labels, and explicit
user-selected model/auth overrides. It drops ambient conversation context such
as channel/group routing, send or queue policy, elevation, origin, and ACP
runtime binding so a fresh isolated run cannot inherit stale delivery or
runtime authority from an older run.

---

## Session keys (`sessionKey`)

A `sessionKey` identifies _which conversation bucket_ you're in (routing + isolation).

Common patterns:

- Main/direct chat (per agent): `agent:<agentId>:<mainKey>` (default `main`)
- Group: `agent:<agentId>:<channel>:group:<id>`
- Room/channel (Discord/Slack): `agent:<agentId>:<channel>:channel:<id>` or `...:room:<id>`
- Cron: `cron:<job.id>`
- Webhook: `hook:<uuid>` (unless overridden)

The canonical rules are documented at [/concepts/session](/concepts/session).

---

## Session ids (`sessionId`)

Each `sessionKey` points at a current `sessionId` (the transcript file that continues the conversation).

Rules of thumb:

- **Reset** (`/new`, `/reset`) creates a new `sessionId` for that `sessionKey`.
- **Daily reset** (default 4:00 AM local time on the gateway host) creates a new `sessionId` on the next message after the reset boundary.
- **Idle expiry** (`session.reset.idleMinutes` or legacy `session.idleMinutes`) creates a new `sessionId` when a message arrives after the idle window. When daily + idle are both configured, whichever expires first wins.
- **System events** (heartbeat, cron wakeups, exec notifications, gateway bookkeeping) may mutate the session row but do not extend daily/idle reset freshness. Reset rollover discards queued system-event notices for the previous session before the fresh prompt is built.
- **Parent fork policy** uses Nodmix's active branch when creating a thread or subagent fork. If that branch is too large, Nodmix starts the child with isolated context instead of failing or inheriting unusable history. The sizing policy is automatic; legacy `session.parentForkMaxTokens` config is removed by `nodmix doctor --fix`.

Implementation detail: the decision happens in `initSessionState()` in `src/auto-reply/reply/session.ts`.

---

## Session store schema (`sessions.json`)

The store's value type is `SessionEntry` in `src/config/sessions.ts`.

Key fields (not exhaustive):

- `sessionId`: current transcript id (filename is derived from this unless `sessionFile` is set)
- `sessionStartedAt`: start timestamp for the current `sessionId`; daily reset
  freshness uses this. Legacy rows may derive it from the JSONL session header.
- `lastInteractionAt`: last real user/channel interaction timestamp; idle reset
  freshness uses this so heartbeat, cron, and exec events do not keep sessions
  alive. Legacy rows without this field fall back to the recovered session start
  time for idle freshness.
- `updatedAt`: last store-row mutation timestamp, used for listing, pruning, and
  bookkeeping. It is not the authority for daily/idle reset freshness.
- `sessionFile`: optional explicit transcript path override
- `chatType`: `direct | group | room` (helps UIs and send policy)
- `provider`, `subject`, `room`, `space`, `displayName`: metadata for group/channel labeling
- Toggles:
  - `thinkingLevel`, `verboseLevel`, `reasoningLevel`, `elevatedLevel`
  - `sendPolicy` (per-session override)
- Model selection:
  - `providerOverride`, `modelOverride`, `authProfileOverride`
- Token counters (best-effort / provider-dependent):
  - `inputTokens`, `outputTokens`, `totalTokens`, `contextTokens`
- `compactionCount`: how often auto-compaction completed for this session key
- `memoryFlushAt`: timestamp for the last pre-compaction memory flush
- `memoryFlushCompactionCount`: compaction count when the last flush ran

The store is safe to edit, but the Gateway is the authority: it may rewrite or rehydrate entries as sessions run.

---

## Transcript structure (`*.jsonl`)

Transcripts are managed by `nodmix/plugin-sdk/agent-sessions`'s `SessionManager`.

The file is JSONL:

- First line: session header (`type: "session"`, includes `id`, `cwd`, `timestamp`, optional `parentSession`)
- Then: session entries with `id` + `parentId` (tree)

Notable entry types:

- `message`: user/assistant/toolResult messages
- `custom_message`: extension-injected messages that _do_ enter model context (can be hidden from UI)
- `custom`: extension state that does _not_ enter model context
- `compaction`: persisted compaction summary with `firstKeptEntryId` and `tokensBefore`
- `branch_summary`: persisted summary when navigating a tree branch

Nodmix intentionally does **not** "fix up" transcripts; the Gateway uses `SessionManager` to read/write them.

---

## Context windows vs tracked tokens

Two different concepts matter:

1. **Model context window**: hard cap per model (tokens visible to the model)
2. **Session store counters**: rolling stats written into `sessions.json` (used for /status and dashboards)

If you're tuning limits:

- The context window comes from the model catalog (and can be overridden via config).
- `contextTokens` in the store is a runtime estimate/reporting value; don't treat it as a strict guarantee.

For more, see [/token-use](/reference/token-use).

---

## Compaction: what it is

Compaction summarizes older conversation into a persisted `compaction` entry in the transcript and keeps recent messages intact.

After compaction, future turns see:

- The compaction summary
- Messages after `firstKeptEntryId`

AGENTS.md section reinjection after compaction is opt-in via
`agents.defaults.compaction.postCompactionSections`; when unset or `[]`,
Nodmix does not append AGENTS.md excerpts on top of the compaction summary.

Compaction is **persistent** (unlike session pruning). See [/concepts/session-pruning](/concepts/session-pruning).

## Compaction chunk boundaries and tool pairing

When Nodmix splits a long transcript into compaction chunks, it keeps
assistant tool calls paired with their matching `toolResult` entries.

- If the token-share split lands between a tool call and its result, Nodmix
  shifts the boundary to the assistant tool-call message instead of separating
  the pair.
- If a trailing tool-result block would otherwise push the chunk over target,
  Nodmix preserves that pending tool block and keeps the unsummarized tail
  intact.
- Aborted/error tool-call blocks do not hold a pending split open.

---

## When auto-compaction happens (Nodmix runtime)

In the embedded Nodmix agent, auto-compaction triggers in two cases:

1. **Overflow recovery**: the model returns a context overflow error
   (`request_too_large`, `context length exceeded`, `input exceeds the maximum
number of tokens`, `input token count exceeds the maximum number of input
tokens`, `input is too long for the model`, `ollama error: context length
exceeded`, and similar provider-shaped variants) → compact → retry.
   When the provider reports the attempted token count, Nodmix forwards that
   observed count into overflow recovery compaction. If the provider confirms
   overflow but does not expose a parseable count, Nodmix passes a minimally
   over-budget synthetic count to compaction engines and diagnostics.
   If overflow recovery still fails, Nodmix surfaces explicit guidance to the
   user and preserves the current session mapping instead of silently rotating
   the session key to a fresh session id. The next step is operator-controlled:
   retry the message, run `/compact`, or run `/new` when a fresh session is
   preferred.
2. **Threshold maintenance**: after a successful turn, when:

`contextTokens > contextWindow - reserveTokens`

Where:

- `contextWindow` is the model's context window
- `reserveTokens` is headroom reserved for prompts + the next model output

These are Nodmix runtime semantics.

Nodmix can also trigger a preflight local compaction before opening the next
run when `agents.defaults.compaction.maxActiveTranscriptBytes` is set and the
active transcript file reaches that size. This is a file-size guard for local
reopen cost, not raw archival: Nodmix still runs normal semantic compaction,
and it requires `truncateAfterCompaction` so the compacted summary can become a
new successor transcript.

For embedded Nodmix runs, `agents.defaults.compaction.midTurnPrecheck.enabled: true`
adds an opt-in tool-loop guard. After a tool result is appended and before the
next model call, Nodmix estimates the prompt pressure using the same preflight
budget logic used at turn start. If the context no longer fits, the guard does
not compact inside Nodmix runtime's `transformContext` hook. It raises a structured
mid-turn precheck signal, stops the current prompt submission, and lets the
outer run loop use the existing recovery path: truncate oversized tool results
when that is enough, or trigger the configured compaction mode and retry. The
option is disabled by default and works with both `default` and `safeguard`
compaction modes, including provider-backed safeguard compaction.
This is independent of `maxActiveTranscriptBytes`: the byte-size guard runs
before a turn opens, while mid-turn precheck runs later in the embedded Nodmix tool
loop after new tool results have been appended.

---

## Compaction settings (`reserveTokens`, `keepRecentTokens`)

Nodmix runtime's compaction settings live in agent settings:

```json5
{
  compaction: {
    enabled: true,
    reserveTokens: 16384,
    keepRecentTokens: 20000,
  },
}
```

Nodmix also enforces a safety floor for embedded runs:

- If `compaction.reserveTokens < reserveTokensFloor`, Nodmix bumps it.
- Default floor is `20000` tokens.
- Set `agents.defaults.compaction.reserveTokensFloor: 0` to disable the floor.
- If it's already higher, Nodmix leaves it alone.
- Manual `/compact` honors an explicit `agents.defaults.compaction.keepRecentTokens`
  and keeps Nodmix runtime's recent-tail cut point. Without an explicit keep budget,
  manual compaction remains a hard checkpoint and rebuilt context starts from
  the new summary.
- Set `agents.defaults.compaction.midTurnPrecheck.enabled: true` to run the
  optional tool-loop precheck after new tool results and before the next model
  call. This is a trigger only; summary generation still uses the configured
  compaction path. It is independent of `maxActiveTranscriptBytes`, which is a
  turn-start active-transcript byte-size guard.
- Set `agents.defaults.compaction.maxActiveTranscriptBytes` to a byte value or
  string such as `"20mb"` to run local compaction before a turn when the active
  transcript gets large. This guard is active only when
  `truncateAfterCompaction` is also enabled. Leave it unset or set `0` to
  disable.
- When `agents.defaults.compaction.truncateAfterCompaction` is enabled,
  Nodmix rotates the active transcript to a compacted successor JSONL after
  compaction. Branch/restore checkpoint actions use that compacted successor;
  legacy pre-compaction checkpoint files remain readable while referenced.

Why: leave enough headroom for multi-turn "housekeeping" (like memory writes) before compaction becomes unavoidable.

Implementation: `ensureAgentCompactionReserveTokens()` in `src/agents/agent-settings.ts`
(called from `src/agents/embedded-agent-runner.ts`).

---

## Pluggable compaction providers

Plugins can register a compaction provider via `registerCompactionProvider()` on the plugin API. When `agents.defaults.compaction.provider` is set to a registered provider id, the safeguard extension delegates summarization to that provider instead of the built-in `summarizeInStages` pipeline.

- `provider`: id of a registered compaction provider plugin. Leave unset for default LLM summarization.
- Setting a `provider` forces `mode: "safeguard"`.
- Providers receive the same compaction instructions and identifier-preservation policy as the built-in path.
- The safeguard still preserves recent-turn and split-turn suffix context after provider output.
- Built-in safeguard summarization re-distills prior summaries with new messages
  instead of preserving the full previous summary verbatim.
- Safeguard mode enables summary quality audits by default; set
  `qualityGuard.enabled: false` to skip retry-on-malformed-output behavior.
- If the provider fails or returns an empty result, Nodmix falls back to built-in LLM summarization automatically.
- Abort/timeout signals are re-thrown (not swallowed) to respect caller cancellation.

Source: `src/plugins/compaction-provider.ts`, `src/agents/agent-hooks/compaction-safeguard.ts`.

---

## User-visible surfaces

You can observe compaction and session state via:

- `/status` (in any chat session)
- `nodmix status` (CLI)
- `nodmix sessions` / `sessions --json`
- Gateway logs (`pnpm gateway:watch` or `nodmix logs --follow`): `embedded run auto-compaction start` + `complete`
- Verbose mode: `🧹 Auto-compaction complete` + compaction count

---

## Silent housekeeping (`NO_REPLY`)

Nodmix supports "silent" turns for background tasks where the user should not see intermediate output.

Convention:

- The assistant starts its output with the exact silent token `NO_REPLY` /
  `no_reply` to indicate "do not deliver a reply to the user".
- Nodmix strips/suppresses this in the delivery layer.
- Exact silent-token suppression is case-insensitive, so `NO_REPLY` and
  `no_reply` both count when the whole payload is just the silent token.
- This is for true background/no-delivery turns only; it is not a shortcut for
  ordinary actionable user requests.

As of `2026.1.10`, Nodmix also suppresses **draft/typing streaming** when a
partial chunk begins with `NO_REPLY`, so silent operations don't leak partial
output mid-turn.

---

## Pre-compaction "memory flush" (implemented)

Goal: before auto-compaction happens, run a silent agentic turn that writes durable
state to disk (e.g. `memory/YYYY-MM-DD.md` in the agent workspace) so compaction can't
erase critical context.

Nodmix uses the **pre-threshold flush** approach:

1. Monitor session context usage.
2. When it crosses a "soft threshold" (below Nodmix runtime's compaction threshold), run a silent
   "write memory now" directive to the agent.
3. Use the exact silent token `NO_REPLY` / `no_reply` so the user sees
   nothing.

Config (`agents.defaults.compaction.memoryFlush`):

- `enabled` (default: `true`)
- `model` (optional exact provider/model override for the flush turn, for example `ollama/qwen3:8b`)
- `softThresholdTokens` (default: `4000`)
- `prompt` (user message for the flush turn)
- `systemPrompt` (extra system prompt appended for the flush turn)

Notes:

- The default prompt/system prompt include a `NO_REPLY` hint to suppress
  delivery.
- When `model` is set, the flush turn uses that model without inheriting the
  active session fallback chain, so local-only housekeeping does not silently
  fall back to a paid conversation model.
- The flush runs once per compaction cycle (tracked in `sessions.json`).
- The flush runs only for embedded Nodmix sessions (CLI backends skip it).
- The flush is skipped when the session workspace is read-only (`workspaceAccess: "ro"` or `"none"`).
- See [Memory](/concepts/memory) for the workspace file layout and write patterns.

Nodmix also exposes a `session_before_compact` hook in the extension API, but Nodmix's
flush logic lives on the Gateway side today.

---

## Troubleshooting checklist

- Session key wrong? Start with [/concepts/session](/concepts/session) and confirm the `sessionKey` in `/status`.
- Store vs transcript mismatch? Confirm the Gateway host and the store path from `nodmix status`.
- Compaction spam? Check:
  - model context window (too small)
  - compaction settings (`reserveTokens` too high for the model window can cause earlier compaction)
  - tool-result bloat: enable/tune session pruning
- Silent turns leaking? Confirm the reply starts with `NO_REPLY` (case-insensitive exact token) and you're on a build that includes the streaming suppression fix.

## Related

- [Session management](/concepts/session)
- [Session pruning](/concepts/session-pruning)
- [Context engine](/concepts/context-engine)
