| name | ctmv3-plugin |
| description | CTMv3 cross-runtime codebase activation engine. Turns any repository into a living, agent-operable workspace in under 60 seconds. Use when activating a new codebase (cold start), resuming an existing CTM session (warm start), detecting topology drift, running the golden-path domino chain, or closing a session with provenance logging. Invokes python3 -m ctmv3 <command>. Replaces sovereign-skill-architect for all CTMv3 plugin operations.
|
CTMv3 PLUGIN SKILL — Cross-Runtime Codebase Activation Engine
Version: 1.3.0
Date: 2026-05-24
Status: Production
Author/Origin: CTMv3 Plugin — gemini-cli/ctmv3/skills/ctmv3/SKILL.md
Replaces: sovereign-skill-architect (docs/SKILL.md, skills/cognitive-topology-v3/SKILL.md)
Table of Contents
- Identity Block
- Quick Start
- Semantic Router
- Command Reference
- Boot State Machine
- Golden-Path Chain Signal Envelope
- Signal Tier Taxonomy
- Failure Grammar — CTMv3 Operational Failures
- Eight Outputs Contract
- Anti-Patterns
- Reference Files
- Install Reference
1. Identity Block
What CTMv3 IS
CTMv3 is a codebase activation system. Its job is to enter any repository and
transform it into a living, agent-operable workspace — in under 60 seconds, with zero
external Python dependencies, using stdlib only, on Python 3.10+.
A single invocation of python3 -m ctmv3 activate on a bare repository produces:
TOPOLOGY.md — cognitive map of the domain (load-bearing concepts, complexity distribution)FAILURE_GRAMMAR.md — what wrong looks like before it is provablePROVENANCE.md — decision log, rejected alternatives, session logARCHITECTURE_MAP.md — traversal map with file:line anchorsAGENTS.md — operational posture document for agent entryCLAUDE.md — Claude-specific context extending AGENTS.md.sovereign/ — session continuity anchor (session_state.json, golden_paths.json, topology_fingerprint.txt).claude/, .codex/, .github/ — dot-directory scaffolds with enforcement hooks
That is the complete set of eight outputs. No more, no less.
What CTMv3 IS NOT
- NOT a skill maker. A skill may be one byproduct; the activated repository is the real output.
- NOT a code generator. It does not produce application code.
- NOT a documentation writer. It produces structural agent infrastructure, not prose.
- NOT a deployment system. It does not push, build, or release anything.
Engine Constraints
| Constraint | Value |
|---|
| Engine version | 1.3.0 |
| Python requirement | 3.10+ |
| External dependencies | Zero (stdlib only) |
| Idempotency | Safe to run activate twice — existing artifacts preserved unless --force |
| Execution time | Under 60 seconds on any normal repository |
| GPU requirement | None |
| Network requirement | None |
The --force flag is the safety valve. Without it, activate will never overwrite
existing artifacts. An agent must pass --force explicitly to overwrite anything.
2. Quick Start
The first three commands any agent needs:
python3 -m ctmv3 version --json
python3 -m ctmv3 boot --project-root "$PWD" --json
python3 -m ctmv3 chain --initial boot --project-root "$PWD"
If step 1 fails, the engine is not installed. See Section 12 (Install Reference).
If step 2 returns COLD_START, the repo has never been activated. Run activate.
If step 2 returns WARM_START, a prior session exists. Run warm to validate and continue.
If step 3 is used, it handles the complete decision sequence automatically. Use step 3
when activating a fresh repo or running a full refresh. Use individual commands when
operating on a specific step.
3. Semantic Router
Classify the task before invoking any command. Load only what the task requires.
Task → Action → Command(s)
──────────────────────────────────────────────────────────────────────────────────
[ENTERING_A_NEW_REPO] — no CTM artifacts present
1. python3 -m ctmv3 boot --project-root "$PWD" --json
Read: {"branch": "COLD_START", "tier1_signals": [], ...}
2. python3 -m ctmv3 activate --project-root "$PWD"
Or shortcut: python3 -m ctmv3 chain --initial boot --project-root "$PWD"
Outcome: all 8 outputs produced; session logged in PROVENANCE.md
[RESUMING_A_SESSION] — CTM artifacts exist, continuing prior work
1. python3 -m ctmv3 warm --project-root "$PWD" --json
Check output: warm_valid == true AND fingerprint_matches == true
2. If warm_valid == false: run activate --force OR investigate PROVENANCE.md
If fingerprint_matches == false: run fingerprint, then architecture-map
3. Proceed with task. Close with session-close.
[CHECKING_DRIFT] — did topology change since last session?
python3 -m ctmv3 fingerprint --project-root "$PWD" --json
If drift_detected == true: run architecture-map, then session-close
If drift_detected == false: proceed directly to session-close
[BUILDING_TRAVERSAL_MAP] — produce ARCHITECTURE_MAP.md from TOPOLOGY.md
python3 -m ctmv3 architecture-map --from-topology --project-root "$PWD"
Prerequisite: TOPOLOGY.md must exist. Run boot first if uncertain.
[CLOSING_A_SESSION] — log work to provenance, anchor state
python3 -m ctmv3 session-close \
--agent "Gemini CLI" \
--action "<brief description of what was done>" \
--next-action "<what the next agent should do>" \
--project-root "$PWD"
Note: Always pass --agent with a real agent identifier. Default "unknown" is
operationally useless and degrades PROVENANCE.md quality.
[CHECKING_STATUS] — what is the current CTM state of this repository?
python3 -m ctmv3 status --project-root "$PWD" --json
Returns: activation status, session state, fingerprint validity, open tasks
[FULL_GOLDEN_PATH] — run the complete activation and close sequence
python3 -m ctmv3 chain --initial boot --project-root "$PWD"
The chain walks: boot → activate (or warm) → fingerprint →
architecture-map (if drift) → session-close
Use this for cold activations and periodic full refreshes.
[FORCE_REACTIVATION] — overwrite existing artifacts intentionally
python3 -m ctmv3 activate --force --project-root "$PWD"
Warning: This overwrites all protected artifacts. Use only when artifacts
are known to be stale, corrupted, or from a different codebase.
[SOMETHING_IS_WRONG] — unexpected behavior, command failure, parse error
1. python3 -m ctmv3 status --project-root "$PWD" --json
2. Load docs/FAILURE_GRAMMAR.md — do this BEFORE any other investigative action
3. Check .sovereign/session_state.json for last known good state
4. If session_state.json is corrupted: delete it and run sovereign-init
5. If artifacts are from a different codebase: activate --force
[ENGINE_NOT_INSTALLED] — python3 -m ctmv3 version fails with ModuleNotFoundError
cd /path/to/ctmv3-plugin/core && pip install -e .
Then verify: python3 -m ctmv3 version --json
Expected output: {"version": "1.3.0", "protocol": "CTMv3"}
[MONOREPO] — multiple subdirectories each have CTM artifacts
Use discover_all() Python API (not a CLI command):
from pathlib import Path
from ctmv3.core.boot import discover_all
inventories = discover_all(Path("."), max_depth=3)
For each inventory: run appropriate command based on inventory.branch
Do NOT run activate on the monorepo root expecting cascade to subdirectories.
See docs/BOOT_PROTOCOL.md Section 7 for full monorepo protocol.
Hard rule: Boot discovery is mandatory before any repo-entry task. The boot signal
inventory is the ground truth for what has already been done.
4. Command Reference
All commands follow this invocation pattern:
python3 -m ctmv3 <subcommand> [--project-root "$PWD"] [--json] [--force] [--no-golden-path]
Global flags available on all subcommands:
| Flag | Effect |
|---|
--project-root PATH | Target repository root (default: current directory) |
--json | Route machine-readable output to stdout; human messages to stderr |
--no-golden-path | Suppress [CTMV3_GOLDEN_PATH] signal emission |
boot
python3 -m ctmv3 boot --project-root "$PWD" [--json] [--no-golden-path]
Purpose: Discovery sequence. Reads the repository read-only. Classifies boot state.
Emits a signal inventory. This command never writes to disk.
JSON output fields:
| Field | Type | Description |
|---|
branch | string | "COLD_START" | "WARM_START" | "PARTIAL" |
tier1_signals | list[str] | Tier 1 paths found (strong CTM presence signals) |
tier2_signals | list[str] | Tier 2 paths found (supporting signals) |
tier3_signals | list[str] | Tier 3 paths found (config spine signals) |
provenance_present | bool | PROVENANCE.md readable at repo root |
manifest_present | bool | manifest.json present (Somnus snapshot lock) |
last_session | str | null | Last PROVENANCE.md Session Log row, or null |
warm_start_valid | bool | Whether warm start conditions are met |
session_state_valid | bool | Whether .sovereign/session_state.json is parseable |
Exit codes:
0 — success1 — user error (project root not found or not a directory)
Golden-path signal: command_status is set to the value of branch.
Agent action: Read branch.
COLD_START → run activateWARM_START → run warmPARTIAL → run activate (consider --force if artifacts are from a different codebase)- Always read the golden-path signal.
next_command_suggested tells you what to run next.
Example:
python3 -m ctmv3 boot --project-root "$PWD" --json
activate
python3 -m ctmv3 activate --project-root "$PWD" [--force] [--json] [--no-golden-path]
Purpose: Cold-start orchestration. Runs Phase 0–5 activation on the repository.
Produces all 8 CTMv3 outputs. The most consequential command in the suite.
JSON output fields:
| Field | Type | Description |
|---|
phase | str | Last completed phase identifier |
project_name | str | Inferred project name (from TOPOLOGY.md, pyproject.toml, or directory) |
files_written | dict[str, str] | Map of absolute path → "created" | "skipped" | "force-overwritten" |
fingerprint | str | SHA-256 hash written to .sovereign/topology_fingerprint.txt |
errors | list[str] | Any non-fatal errors encountered (check this even on exit code 0) |
aborted | bool | True if activation was halted by the guard (artifacts exist, no --force) |
abort_reason | str | null | Human-readable abort reason if aborted=true |
signal_inventory | dict | Full boot.discover() output at time of activation |
today | str | ISO date used in rendered templates |
Exit codes:
0 — success (all artifacts produced)1 — user error (project root invalid)2 — corrupt state detected in repository
Guard behavior: If WARM_START or PARTIAL state is detected AND protected artifacts
already exist AND --force is not passed, activation aborts and returns {aborted: true, abort_reason: "..."}. This is intentional. The guard prevents silent overwrites.
Agent action: Check aborted first. If true, read abort_reason. If artifacts exist
and the repo needs a full reset, pass --force. Otherwise run warm instead.
Example:
python3 -m ctmv3 activate --project-root "$PWD" --json
warm
python3 -m ctmv3 warm --project-root "$PWD" [--json] [--no-golden-path]
Purpose: Warm-start validation. Runs the three warm-validity checks against the
existing session state. Does not write any topology artifacts. May update session state.
JSON output fields:
| Field | Type | Description |
|---|
warm_valid | bool | True if all three warm validity checks pass |
fingerprint_matches | bool | Current topology hash matches stored hash |
session_age_days | float | Days since last session close |
last_session | str | null | Last PROVENANCE.md Session Log entry |
checks | dict | {topology_valid, provenance_coherent, no_rejected_path_active} |
warnings | list[str] | Non-blocking conditions worth noting |
Exit codes:
0 — success (warm check ran, regardless of warm_valid value)1 — user error3 — no artifacts to warm (cold repository — run activate first)
Warm validity criteria (all three must pass for warm_valid = true):
- Topology still valid — no significant code change since last encoding
- Provenance coherent — Session Log last action matches current AGENTS.md / ARCHITECTURE_MAP.md state
- No rejected path in play — current task does not match PROVENANCE.md Graveyard entries
Agent action: If warm_valid == true and fingerprint_matches == true, proceed with
the task. If warm_valid == false, run activate --force or investigate PROVENANCE.md.
If fingerprint_matches == false, run fingerprint then architecture-map.
fingerprint
python3 -m ctmv3 fingerprint --project-root "$PWD" [--json] [--no-golden-path]
Purpose: Recompute the SHA-256 topology fingerprint from TOPOLOGY.md and
ARCHITECTURE_MAP.md. Compare against stored hash to detect drift. Write new hash to
.sovereign/topology_fingerprint.txt.
Fingerprint scope: Only TOPOLOGY.md and ARCHITECTURE_MAP.md are hashed (concatenated,
in that order). Changes to other CTMv3 artifacts do not affect the fingerprint. This is
intentional — the fingerprint tracks topology drift, not session state drift.
JSON output fields:
| Field | Type | Description |
|---|
drift_detected | bool | True if stored hash differs from newly computed hash |
old_hash | str | null | Previously stored hash, or null if absent |
new_hash | str | Newly computed hash |
files_hashed | list[str] | Files included in the computation |
fingerprint_path | str | Absolute path of the written fingerprint file |
Exit codes: 0 success, 1 user error
Golden-path signal: command_status is "drift_detected" or "no_drift".
Agent action: If drift_detected == true, run architecture-map to refresh the
traversal map, then session-close. If drift_detected == false, run session-close
directly.
architecture-map
python3 -m ctmv3 architecture-map --project-root "$PWD" [--from-topology] [--force] [--json] [--no-golden-path]
Purpose: Build or update ARCHITECTURE_MAP.md — the traversal map artifact. With
--from-topology, reads TOPOLOGY.md H1 header to infer project name. Without
--from-topology, uses the project name inference chain (TOPOLOGY.md → pyproject.toml
→ package.json → go.mod → directory name).
JSON output fields:
| Field | Type | Description |
|---|
map_path | str | Absolute path of written ARCHITECTURE_MAP.md |
status | str | "created" | "skipped" | "force-overwritten" |
project_name | str | Inferred project name used in template |
Exit codes: 0 success, 1 user error
Agent action: Verify map_path exists after command completes. Open and review the
generated map — it contains [TODO: ...] placeholders that require agent population
based on the actual codebase structure.
sovereign-init
python3 -m ctmv3 sovereign-init --project-root "$PWD" [--json] [--no-golden-path]
Purpose: Initialize the .sovereign/ directory with session_state.json,
golden_paths.json, and topology_fingerprint.txt placeholder. Safe to run on a
fresh repository. If .sovereign/ already exists and session_state.json is valid,
does not overwrite.
JSON output fields:
| Field | Type | Description |
|---|
sovereign_path | str | Absolute path of .sovereign/ |
files_created | dict[str, str] | Map of filename → status |
session_id | str | UUID4 of the initialized session |
Exit codes: 0 success, 1 user error
Agent action: Normally invoked by activate. Run directly only when recovering
from a corrupted .sovereign/ directory.
dot-init
python3 -m ctmv3 dot-init --project-root "$PWD" [--targets all|claude|codex|github] [--force] [--json] [--no-golden-path]
Purpose: Create or update the .claude/, .codex/, and .github/ scaffold
directories. Each target is independent. Default --targets all creates all three.
Created artifacts:
.claude/settings.json — Claude Code permission configuration.claude/CLAUDE.md — Claude-specific context (skipped if root CLAUDE.md exists).codex/skills/.gitkeep — Codex skill installation anchor.codex/session/ — Codex session directory.github/copilot-instructions.md — Repo-wide agent instruction surface.github/instructions/README.md — Per-path instructions index.github/workflows/topology-enforce.yml — CTMv3 fingerprint drift CI gate
JSON output fields:
| Field | Type | Description |
|---|
files_created | dict[str, str] | Map of absolute path → status |
targets_run | list[str] | Which targets were initialized |
Exit codes: 0 success, 1 user error
Agent action: After dot-init, verify the .github/workflows/topology-enforce.yml
is present and correct before committing. Never build .github/ before TOPOLOGY.md is
complete — the hooks enforce topology contracts, and topology must be known before
enforcement is defined.
session-close
python3 -m ctmv3 session-close \
--agent "Gemini CLI" \
--action "<description>" \
--next-action "<recommendation>" \
[--topology-drift] \
--project-root "$PWD" \
[--json] \
[--no-golden-path]
Purpose: Close the session cleanly. Updates PROVENANCE.md Session Log with the
completed action and next recommended action. Rewrites .sovereign/session_state.json
with warm_start_valid = true. Recomputes and stores the topology fingerprint.
This is the provenance anchor. A session without a clean close leaves orphaned state
that degrades the next agent's warm-start accuracy.
JSON output fields:
| Field | Type | Description |
|---|
agent | str | Agent identifier as passed |
action | str | Action description as passed |
topology_drift | bool | Whether drift was flagged |
fingerprint | str | SHA-256 hash written at close |
provenance_updated | bool | Whether PROVENANCE.md was updated |
session_state_updated | bool | Whether session_state.json was updated |
Exit codes: 0 success, 1 user error
Session log rotation: When PROVENANCE.md Session Log exceeds 500 rows, older rows
are automatically archived to .sovereign/provenance_archive_{date}.md. The active
log retains the 100 most recent rows. This is transparent to the agent.
Agent action: Always pass --agent with a real identifier. Pass --topology-drift
if TOPOLOGY.md was modified during the session. The --next-action value becomes the
first thing the next agent reads from PROVENANCE.md.
status
python3 -m ctmv3 status --project-root "$PWD" [--json] [--no-golden-path]
Purpose: Print a current snapshot of the repository's CTMv3 activation state.
Does not write anything. Useful as a diagnostic before any other command.
JSON output fields:
| Field | Type | Description |
|---|
activated | bool | Whether the repository has been CTMv3 activated |
branch | str | Current boot classification |
fingerprint_valid | bool | Whether stored fingerprint matches current topology |
session_age_days | float | null | Days since last session close |
last_agent | str | null | Agent that last closed a session |
last_action | str | null | Last logged action |
open_tasks | list[str] | Open tasks from session_state.json |
artifacts_present | dict[str, bool] | Map of artifact name → present |
Exit codes: 0 success, 1 user error
Agent action: Run status as the first command when investigating unexpected
behavior. It provides the complete current state without writing anything.
version
python3 -m ctmv3 version [--json]
Purpose: Print the engine version. The most lightweight verification that the
engine is installed and functional.
JSON output fields:
| Field | Type | Description |
|---|
version | str | Engine version string (e.g., "1.3.0") |
protocol | str | Protocol identifier ("CTMv3") |
Exit codes: 0 success, 1 engine not installed (ModuleNotFoundError)
Agent action: Run this first in any automation that depends on CTMv3. If it
fails, run the install sequence from Section 12 before proceeding.
chain
python3 -m ctmv3 chain \
--initial boot \
--project-root "$PWD" \
[--no-golden-path]
Purpose: Execute the full golden-path domino chain from a specified initial command.
Each command in the chain runs as a subprocess. The pre-chain rules table determines
which command runs next based on the exit state of the previous command. The chain
terminates when no next command exists (terminal state) or when MAX_CHAIN_DEPTH = 5
is reached.
Chain output: Stdout is a JSON array. Each element is one step's signal dict with
a chain_depth field indicating step index (0-based). Individual step signals are also
emitted under the [CTMV3_GOLDEN_PATH] sentinel as the chain progresses.
Exit codes:
0 — chain completed successfully (all steps terminated normally)1 — user error2 — chain exceeded MAX_CHAIN_DEPTH (5 steps); run commands individually
Agent action: Parse stdout as a JSON array. Each element has command_name,
command_status, next_command_suggested, memory_relevance_tags, payload, and
chain_depth. The chain is the preferred entry point for cold activations and full
refreshes. For targeted operations (e.g., only checking drift), run individual commands.
Important: The chain uses --no-golden-path internally when invoking subprocess
steps to prevent double-emission of signals. The outer chain call collects all signals
and re-emits them at chain completion. Do not pass --no-golden-path to chain itself
unless you want to suppress the aggregated output.
5. Boot State Machine
stateDiagram-v2
[*] --> Discovery: boot command
Discovery --> COLD_START: No Tier 1 signals found
Discovery --> PARTIAL: Tier 1 signals present, PROVENANCE.md absent or Session Log empty
Discovery --> WARM_START: Tier 1 signals + PROVENANCE.md + recent Session Log entry
COLD_START --> Activation: activate
PARTIAL --> Activation: activate (--force optional)
WARM_START --> WarmCheck: warm
Activation --> Fingerprint: activate success
WarmCheck --> Fingerprint: warm_valid=true, fingerprint_matches=true
WarmCheck --> Fingerprint: warm_valid=true, fingerprint_matches=false
WarmCheck --> ForceActivation: warm_valid=false AND session stale
ForceActivation --> Fingerprint: activate --force success
Fingerprint --> DriftPath: drift_detected=true
Fingerprint --> SessionClose: no_drift=true
DriftPath --> ArchMap: architecture-map
ArchMap --> SessionClose: architecture-map success
SessionClose --> [*]: session-close success
State transition rules (encoded in orchestration.py:pre_chain_rules):
| From state | Exit condition | Next state |
|---|
| boot | COLD_START | activate |
| boot | WARM_START | warm |
| boot | PARTIAL | activate |
| activate | success | fingerprint |
| activate | failure | (terminal — investigate) |
| warm | success | fingerprint |
| warm | failure | (terminal — investigate) |
| fingerprint | drift_detected | architecture-map |
| fingerprint | no_drift | session-close |
| architecture-map | success | session-close |
| architecture-map | skipped | session-close |
| session-close | success | (terminal) |
| sovereign-init | success | dot-init |
| dot-init | success | fingerprint |
The chain terminates at any failure exit state for most commands. failure is not
chained — it is a signal to investigate before proceeding.
6. Golden-Path Chain Signal Envelope
Every CTMv3 subcommand emits exactly one signal to stdout after completing. The signal
is a single line beginning with the sentinel prefix [CTMV3_GOLDEN_PATH].
Signal Format
[CTMV3_GOLDEN_PATH] {
"command_name": "boot",
"command_status": "COLD_START",
"next_command_suggested": "activate",
"memory_relevance_tags": ["activation", "cold_start", "phase_0_required", "no_tier1_signals"],
"payload": {"branch": "COLD_START", "tier1_signals": [], "tier2_signals": [], ...},
"chain_depth": 0
}
Signal properties:
| Field | Type | Description |
|---|
command_name | str | Name of the command that just completed |
command_status | str | Exit state of the command (e.g., COLD_START, drift_detected) |
next_command_suggested | str | null | Next command to run, or null if terminal |
memory_relevance_tags | list[str] | Tags for memory system indexing |
payload | dict | Full JSON output of the command |
chain_depth | int | Step index in a chain run (0 for standalone commands) |
Extracting Signals
output=$(python3 -m ctmv3 boot --project-root "$PWD" --json)
signal=$(echo "$output" | grep "^\[CTMV3_GOLDEN_PATH\]" | sed 's/^\[CTMV3_GOLDEN_PATH\] //')
next_cmd=$(echo "$signal" | python3 -c "import sys, json; d=json.load(sys.stdin); print(d.get('next_command_suggested',''))")
echo "Next suggested command: $next_cmd"
import subprocess, json
lines = subprocess.check_output(
["python3", "-m", "ctmv3", "boot", "--json", "--project-root", "/path/to/repo"]
).decode().splitlines()
SENTINEL = "[CTMV3_GOLDEN_PATH]"
signals, json_lines = [], []
for line in lines:
if line.startswith(SENTINEL):
signals.append(json.loads(line[len(SENTINEL):].strip()))
else:
json_lines.append(line)
signal = signals[0] if signals else None
if signal and signal["next_command_suggested"]:
print(f"Suggested next: {signal['next_command_suggested']!r}")
Pre-Chain Rules Table
| Command | Exit State | Next Suggested |
|---|
| boot | COLD_START | activate |
| boot | WARM_START | warm |
| boot | PARTIAL | activate |
| boot | success | warm |
| boot | failure | (terminal) |
| activate | success | fingerprint |
| activate | failure | (terminal) |
| warm | success | fingerprint |
| warm | failure | (terminal) |
| fingerprint | drift_detected | architecture-map |
| fingerprint | no_drift | session-close |
| fingerprint | success | session-close |
| fingerprint | failure | (terminal) |
| architecture-map | success | session-close |
| architecture-map | skipped | session-close |
| architecture-map | failure | (terminal) |
| session-close | success | (terminal) |
| session-close | failure | (terminal) |
| sovereign-init | success | dot-init |
| sovereign-init | failure | (terminal) |
| dot-init | success | fingerprint |
| dot-init | failure | (terminal) |
| status | success | (terminal) |
Memory Relevance Tags
Common tag sets for the most important states:
| Command + State | Tags |
|---|
| boot / COLD_START | activation, cold_start, phase_0_required, no_tier1_signals |
| boot / WARM_START | activation, warm_start, tier1_signals_present, provenance_valid |
| boot / PARTIAL | activation, partial_state, tier1_present, provenance_absent |
| activate / success | activation, phase_0_5_complete, all_artifacts_written, repo_live |
| fingerprint / drift_detected | topology, fingerprint_drift, architecture_map_stale |
| fingerprint / no_drift | topology, fingerprint_stable, no_drift |
| session-close / success | session, close_complete, provenance_updated, state_anchored |
Full table: docs/interfaces/orchestration.md.
Suppressing Signals
Use --no-golden-path to suppress signal emission entirely. This is appropriate for:
- Environments that parse stdout and cannot tolerate extra lines
- Nested subprocess calls where double-emission is a concern
- Scripting contexts where the signal format is not needed
The chain command internally passes --no-golden-path to subprocess steps.
7. Signal Tier Taxonomy
The boot discovery sequence classifies found files into three tiers. Tier classification
drives the branch determination.
Tier 1 — Strong CTM Presence Signals
Any single Tier 1 signal means CTMv3 has been run here. No Tier 1 signals means COLD_START.
| Path | What It Signals |
|---|
.sovereign/ | Sovereign session state directory exists; warm start likely |
ARCHITECTURE_MAP.md | Full traversal map was produced; agent can navigate |
.claude/CLAUDE.md | Claude Code context was set up by CTMv3 |
AGENTS.md | Agent operational posture was encoded |
Tier 2 — Supporting Signals
Tier 2 signals indicate partial CTM activation or related tooling presence.
| Path | What It Signals |
|---|
.github/copilot-instructions.md | dot-init was run (or equivalent) |
.codex/skills/ | Codex skill installation is present |
PROVENANCE.md (at repo root) | Decision log was initialized; session history exists |
manifest.json | Somnus snapshot lock — file set is version-pinned |
golden_paths.json | bb7 system golden paths present at repo root |
Tier 3 — Config Spine Signals
Tier 3 signals are always present in real projects. They are read during archaeology, not
used for branch classification. They reveal the project structure before any source is read.
| Path | What It Reveals |
|---|
pyproject.toml / setup.py | Python dependency graph, entry points, tool config |
go.mod | Go import graph canonical prefix, version constraints |
Cargo.toml | Rust binary entry points (each [[bin]] is a topology node) |
package.json | Node.js project name, scripts, dependency graph |
.env.example | Environment variable requirements without exposing secrets |
Branch Classification Logic
COLD_START: len(tier1_signals) == 0
WARM_START: len(tier1_signals) >= 1 AND provenance_present AND last_session is not None AND session age < 30 days
PARTIAL: len(tier1_signals) >= 1 AND (NOT provenance_present OR last_session is None)
The boot command encodes this logic in boot.py:classify_branch(). The branch
determination is deterministic given the same repository state.
8. Failure Grammar — CTMv3 Operational Failures
When something goes wrong, load docs/FAILURE_GRAMMAR.md immediately, before any other
investigative action. The table below covers CTMv3-specific operational failures.
The full failure grammar (pre-failure signatures, false success patterns, adversarial
signatures) is in docs/FAILURE_GRAMMAR.md.
| Failure Signature | Meaning | Recovery Command |
|---|
warm returns warm_valid=false | Session state stale (>30 days) or topology has drifted beyond the warm threshold | activate --force OR investigate PROVENANCE.md Graveyard for rejected paths |
warm returns exit code 3 | No artifacts to warm — repository is cold (no Tier 1 signals) | Run activate first |
fingerprint returns drift_detected=true | TOPOLOGY.md or ARCHITECTURE_MAP.md changed since last fingerprint write | Run architecture-map, then session-close |
activate returns aborted=true | Protected artifacts exist, --force was not passed | Read abort_reason; pass --force if overwrite is appropriate |
activate exits code 2 | Corrupt state detected in repository | Inspect .sovereign/ files; run sovereign-init to reseed |
chain exits code 2 | Chain exceeded MAX_CHAIN_DEPTH (5 steps) | Run commands individually per the pre-chain rules table |
boot shows PARTIAL | Tier 1 signals present but PROVENANCE.md absent or Session Log empty | Run activate OR manually create PROVENANCE.md and initialize Session Log |
.sovereign/session_state.json parse error | File corrupted mid-write (process killed during write) | Delete session_state.json; run sovereign-init to reseed |
python3 -m ctmv3 version fails with ModuleNotFoundError | Engine not installed in current Python environment | cd /path/to/ctmv3-plugin/core && pip install -e . |
python3 -m ctmv3 version fails with ImportError | Engine installed but import is broken (dependency issue) | Verify stdlib only; check Python version is 3.10+ |
session-close does not update PROVENANCE.md | PROVENANCE.md section header missing or file structure corrupted | Read PROVENANCE.md; verify ## Session Log section exists with table header row |
AGENTS.md references non-existent modules | AGENTS.md was copy-pasted or written before topology was known | Rebuild AGENTS.md from TOPOLOGY.md per docs/AGENTS_ADDENDUM.md |
| ARCHITECTURE_MAP.md line anchors wrong | Code was refactored after map was built | Run architecture-map --force to rebuild |
session_state.json warm_start_valid=true but topology clearly changed | File was not updated at last session close (orphaned session) | Run fingerprint to recompute, then session-close |
.github/ hooks failing on every CI run | Topology constraint encoded in hook is outdated | Update the hook; update TOPOLOGY.md Baked-In Decisions; log in PROVENANCE.md |
Ecosystem failure taxonomy (from docs/FAILURE_GRAMMAR.md Category 5):
| Smell | Severity | Action |
|---|
| AGENTS.md references non-existent modules | HIGH | Full AGENTS.md rebuild from TOPOLOGY.md |
| ARCHITECTURE_MAP.md line anchors wrong | MEDIUM | Anchor audit + architecture-map --force |
| session_state.json warm_start_valid=true but session is stale | HIGH | Run BOOT_PROTOCOL.md §3.1 warm validity check |
| .github/ hooks failing on every PR | MEDIUM | Update hook, update TOPOLOGY.md, log in PROVENANCE.md |
| CLAUDE.md and AGENTS.md diverged | HIGH | Reconcile from AGENTS.md (canonical); CLAUDE.md extends, never contradicts |
9. Eight Outputs Contract
A completed CTMv3 pass produces exactly 8 outcomes. An agent must be able to verify
all 8 before declaring activation complete. If any are missing, the activation is
incomplete — do not declare success.
Verification checklist:
| # | Output | How to Verify | Source Document |
|---|
| 1 | Agent can answer: what are the 3 things I cannot get wrong? | Read TOPOLOGY.md — Load-Bearing Concepts section must have 3+ LBC entries with definitions and common misunderstandings | TOPOLOGY.md |
| 2 | Agent can recognize failure before it is provable | Read FAILURE_GRAMMAR.md — Pre-Failure Signatures section must be populated for this codebase | FAILURE_GRAMMAR.md |
| 3 | Agent knows what was already rejected | Read PROVENANCE.md — Rejected Alternatives (Graveyard) section must be present (may be empty on first activation) | PROVENANCE.md |
| 4 | Agent knows where complexity concentrates | Read ARCHITECTURE_MAP.md — DENSE/MEDIUM/THIN markings must be present on file entries | ARCHITECTURE_MAP.md |
| 5 | Agent knows its entry vector | Read AGENTS.md — semantic router section with task-type-to-entry-point table must be present | AGENTS.md |
| 6 | Agent knows boot state in <60 seconds | Run python3 -m ctmv3 boot --project-root "$PWD" --json — must return branch in <60s | boot command |
| 7 | Agent has a traversal map | Read ARCHITECTURE_MAP.md — must have ROOT node, branch entries, and file:line anchors | ARCHITECTURE_MAP.md |
| 8 | Codebase enforces itself | Verify .github/workflows/topology-enforce.yml exists AND .sovereign/topology_fingerprint.txt exists | .github/, .sovereign/ |
Note on Output 1: The LBC entries in TOPOLOGY.md are scaffolded with [TODO: ...]
placeholders on cold activation. An agent must populate these from actual codebase
archaeology before Output 1 is considered satisfied. A scaffolded but unpopulated
TOPOLOGY.md does not satisfy Output 1.
Note on Output 4: The ARCHITECTURE_MAP.md template includes DENSE/MEDIUM/THIN
markers as placeholders. These must be filled by the agent based on actual file analysis.
10. Anti-Patterns
Operational anti-patterns. Violating these degrades reliability and provenance integrity.
Do NOT run activate on a WARM_START repository without --force.
The guard will abort and return {aborted: true}. This is not a bug. If you need to
reset a warm-start repo, pass --force explicitly and understand that it will overwrite
all protected artifacts.
Do NOT ignore the golden-path signal.
The next_command_suggested field exists for a reason. Following it is not mandatory,
but ignoring it consistently means you are running commands in a suboptimal order and
missing drift signals.
Do NOT call session-close with --agent omitted or set to the default "unknown".
The PROVENANCE.md Session Log is the continuity anchor between sessions. An entry with
agent="unknown" is not useful to the next agent. Always pass a real agent identifier.
Do NOT modify .sovereign/session_state.json manually.
This file is managed by session-close and sovereign-init. Manual edits risk leaving
the file in a state that parse checks will reject on next boot, degrading to COLD_START.
Do NOT confuse CTMv3 with a skill maker.
CTMv3 produces activated repositories, not skill packages. Skills are an optional
byproduct of the activation process. If you are trying to build a skill, read
docs/SKILL.md and docs/TOPOLOGY.md — those are the correct references.
Do NOT run activate twice on a fresh repo expecting the second run to repair a
partial first activation.
The second run will abort (artifacts exist, no --force). To repair a partial
activation, pass --force on the second run.
Do NOT skip session-close.
PROVENANCE.md is the continuity anchor. A session without a close leaves orphaned
provenance — the next agent's warm check will see an outdated last session entry and
may misclassify the boot state.
Do NOT run activate before boot.
Always run boot first to establish the current branch. Running activate on a
WARM_START repo without knowing its state risks either aborting (no --force) or
overwriting valid artifacts (with --force). The boot signal inventory is the ground
truth.
Do NOT populate TOPOLOGY.md templates with generic content.
The LBC entries, complexity distribution, and baked-in decisions in TOPOLOGY.md must
be derived from actual codebase archaeology. Copy-pasted or pattern-matched content
in TOPOLOGY.md produces AGENTS.md entries that reference non-existent modules —
Ecosystem Failure 1 from docs/FAILURE_GRAMMAR.md.
Do NOT build .github/ enforcement before TOPOLOGY.md is complete.
The hooks enforce topology contracts. Topology must be known before enforcement is
defined. Hook-first is enforcement without definition.
11. Reference Files
Load only what the task requires. Do not load all reference files upfront.
| Task | Load |
|---|
| Any repo entry (always first) | docs/BOOT_PROTOCOL.md |
| Understanding what CTMv3 does | docs/EXPLANATION.md |
| Building topology artifacts manually | docs/TOPOLOGY.md |
.xyz directory work | docs/DOT_TOPOLOGY.md |
| Something is wrong (immediately) | docs/FAILURE_GRAMMAR.md |
| Architectural disputes, development philosophy | docs/CONSTITUTION.md |
| Building or updating traversal maps | docs/ARCHITECTURE_MAP_TEMPLATE.md |
| Orchestration signal details | docs/interfaces/orchestration.md |
| Cross-runtime adapter format reference | research/RUNTIME_FORMATS.md |
| Schema audit across all 5 adapters | docs/SCHEMA_AUDIT.md |
| Codebase architectural intelligence | CODEBASE_INTELLIGENCE.md |
| AGENTS.md construction | docs/AGENTS_ADDENDUM.md |
| Annotated cold-start trace | examples/cold-start-trace.md |
| Decision log doctrine | docs/PROVENANCE.md |
| This plugin skill (canonical) | gemini-cli/ctmv3/skills/ctmv3/SKILL.md (this file) |
Priority ordering for conflict resolution:
- This SKILL.md (plugin-mode canonical reference)
docs/BOOT_PROTOCOL.md (state machine authority)docs/GOLDEN_PATH.md (orchestration authority)docs/CONSTITUTION.md (development philosophy authority)
If gemini-cli/ctmv3/skills/ctmv3/SKILL.md and docs/SKILL.md conflict on a command
invocation, this file takes precedence. docs/SKILL.md is the manual-mode fallback.
12. Install Reference
Engine Installation (Required for all adapters)
cd /path/to/ctmv3-plugin/core
pip install -e .
pip install .
python3 -m ctmv3 version --json
Gemini CLI Adapter Installation
bash /path/to/ctmv3-plugin/gemini-cli/install.sh
Environment Variable Override
export CTMV3_PROJECT_ROOT="/path/to/your/project"
bash /path/to/ctmv3-plugin/gemini-cli/ctmv3/scripts/ctmv3-wrap.sh boot
Quick Activation From Any Project
cd /your/project
python3 -m ctmv3 version --json
python3 -m ctmv3 chain --initial boot --project-root "$PWD"
python3 -m ctmv3 status --project-root "$PWD" --json
Monorepo Installation Note
CTMv3 is installed once and operates on multiple repositories independently. The engine
does not need to be installed inside each repository — it is invoked from wherever it
is installed with --project-root pointing to the target repository.
For monorepo activation of subdirectories, use the discover_all() Python API rather
than running the CLI sequentially. See docs/BOOT_PROTOCOL.md Section 7.
End of CTMv3 Plugin SKILL.md — Version 1.3.0 — 2026-06-12
