# Generated reports (scripts/)
scripts/coverage_report.json
scripts/calibration_report.json

# Working corpus (historical reconciliation artifacts)
reconcile all/

# Auto-accelerator runtime state
.auto_accelerator_state.json

# Runtime-generated state files (EP-NOISE-CONFLICT class, S2026-04-28d)
# These are produced by PULSE, GDS, audit, scheduler, and synergy runs.
# Tracked historically; now untracked because they create noise merge
# conflicts on every branch divergence (verified via PR #356 diagnosis).
# Each has at least one Python writer that regenerates it on next run.
.gds_remediation.lock
agents/artifacts/backlog_verification_latest.json
state/pulse/auto/
state/pulse/patent/last_board.json
state/pulse/patent/last_output.json
state/pulse/patent/last_pulse.json
state/scheduler/last_board.json
state/scheduler/last_bridge.json
state/scheduler/last_pulse.json
state/scheduler/last_output.md
state/data/audit_runs/last_run.json
agents/topology/docs/run_history.json
.claude/skills_archive/synergy/last_sweep.json

# Audio/media binaries
*.m4a
*.mp3
*.wav
*.mp4

# Python
__pycache__/
*.py[cod]
*.pyo
*.pyd
.venv/
venv/
.pytest_cache/
.mypy_cache/
.ruff_cache/
.tox/
*.egg-info/
dist/
build/

# Environment & Secrets
.env
.env.*
!.env.example
.mcp.json

# macOS
.DS_Store

# Node
node_modules/

# Next.js / OpenNext build output (do not let local builds pollute status).
# Note: some saas/apps/store/.next paths may already be tracked historically —
# this ignore only suppresses *untracked* build churn; untrack is a separate PR.
**/.next/
**/.open-next/
!.nextos/

# Cloned repos (for package resolution)
repos/
vendor/
third_party/

# Cloudflare
.wrangler/

# Logs
*.log
logs/

# Runtime artifacts (execution telemetry)
telemetry/
test_telemetry/
.thriven/

# Ephemeral scan/worker state (regenerable)
var/

# Local backups (not needed in repo)
.backups/

# Data exports (regeneratable from SQL)
layer3/workers/corpus-mcp/*.csv

# One-time analysis scripts
analysis/

# Nested directories (accidental)
projects/NextOS/

# Auto-generated CLAUDE.md files (claude-mem metadata)
# Keep root CLAUDE.md, ignore subdirectory ones
**/*/CLAUDE.md

# Cognitive state telemetry (project-scoped, ephemeral)
.nextos/

# NextOS XML tooling artifacts
runs/
output.xml
response.json
options.xml
*.zip

# Reference documents (not source)
*Reference*.txt

# === BLOAT PREVENTION (added 2026-01-19) ===

# Runtime databases (regenerable)
postgres/
*.db

# Analysis outputs (regenerable)
repo_analysis/
runs/p0_claims/

# Build artifacts
output.xml
options.xml
response.json

# Archive files (should not be versioned)
*.zip

# === PHASE 5 BLOAT PREVENTION (added 2026-01-19) ===

# Generated SVG diagrams (regenerable from .puml)
*.svg

# Runtime artifacts
runs/
excavation/

# Historical backups (superseded)
.backups/

# Python cache (already had __pycache__/, adding explicit)
*.pyc
*.pyo
.env.session

# never commit raw resources
raw resources/
chats/
audit/anthropic_usage_scan.txt

# Claude settings backups
.claude/*.bak.*

# Session transcripts
*.txt
.claude/transcripts/
patterns.jsonl
# Raw session-transcript exports carry pasted key material — LOCAL-ONLY, never commit (S2026-06-03)
state/exports/*TRANSCRIPT*.jsonl
state/exports/*TRANSCRIPT*.jsonl.gz
state/exports/SESSION_TRANSCRIPT_*
# Local-scratch engram/session memory (24.8K files) — not version-controlled on this scratch host (S2026-06-03)
memory/
/corpus/

# Foundation corpus (cloned repos for claim extraction)
foundation/

# Generated claim files (regenerable from extraction scripts)
foundation_claims.jsonl
foundation_import.cypher
foundation_stats.json

# Runtime data (classification receipts, etc.)
state/data/*
# Exceptions: tracked lifecycle data
!state/data/skill_pagerank_ranking.json
!state/data/audit_runs/
!state/data/bio/

# Skill parity reconciliation receipt log (runtime, regenerable)
# Canonical schema lives at agents/source/docs/SKILL_PARITY_RECEIPT_SCHEMA.md
state/governance/skill_parity.jsonl
state/governance/skill_parity_schema.md
.archive/

# Archived/external - do not recreate
repos/
foundation/
.archive/
*.pdf
!docs/patent/drawings/*.pdf

# === WORKING TREE OPTIMIZATION (2026-02-07) ===

# Cloned reference repos (18 nested git repos, ~5GB total)
# These are reference/research clones, not project dependencies.
# If any become dependencies, convert to git submodules.
# supabase/ tracked (init + types + schema)
litellm/
claude-cookbooks/
node/
promptfoo/
n8n-docs/
n8n-hosting/
n8n-mcp/
n8n-nodes-starter/
n8n-workflows/
awesome-n8n-templates/
NodeGraphProcessor/
graph-node/
claude-code/
claude-code-monitoring-guide/
autocache/
agentskills/
Dockerfile-tmux/

# Backup files
*.sql.bak
*.bak

# Data artifacts (regenerable / ephemeral)
cascade_comparison.json
cascade_comparator.jsx
thriven_dump.sql
wiretap_events.jsonl
skills_v1.json
compass_artifact_wf-*.md

# Root-level prototype scripts (not part of core)
# Both old (thriven_*) and new (thesrc_*) names ignored
thriven_wiretap.py
thesrc_wiretap.py
thriven_profiler.py
thesrc_profiler.py
thriven_profiler_consumer.py
thesrc_profiler_consumer.py
thriven_observer.py
thesrc_observer.py
thriven_laboratory.py
thesrc_laboratory.py
aggregate_cascade.py
thriven_chain_hud.jsx
thesrc_chain_hud.jsx
thriven_composition_hud.jsx
thesrc_composition_hud.jsx
thriven_hud.jsx
thesrc_hud.jsx
thriven_arch_diff.jsx
thesrc_arch_diff.jsx
thriven_graph_implications.jsx
thesrc_graph_implications.jsx
thriven_live_state_v3.jsx
thesrc_live_state_v3.jsx
thriven-hud-watch
thesrc-hud-watch

# Root-level scratch docs (not part of core)
ARCHITECTURE_COMPONENT.md
ARCHITECTURE_COMPONENT_v*.md

# Claude.ai artifacts (skill inventory, spec docs)
thriven_optimal_skill_system.jsx
thesrc_optimal_skill_system.jsx
COMPOSITIONAL_COGNITIVE_GRAPH_SPEC*.md
LAYERED_VARIANCE_MODEL*.md

# HUD — track source, ignore build artifacts and binaries
HUD/dist/
HUD/node_modules/
HUD/.wrangler/
HUD/.env*
HUD/.DS_Store
HUD/*.db
HUD/*.zip
HUD/*.rtf
HUD/*.png
HUD/*.jsonl
HUD/HUDs/
HUD/HUDs.zip
HUD/thesrc-hud-watch
# But track the curated design assets in docs/hud/
!docs/hud/

# Vendor themes (audit artifacts, not source)
core/audit/Thrive Web/

# Misc config artifacts
.prettierrc
.prettierignore
agentic_gap_closure.md

# === S203 GAP CLOSURE (2026-02-20) ===

# Claude Code session metadata (per-project, ephemeral)
# Memory files within are force-added by session-end hook (S2026-04-06 split-state fix)
.claude/projects/

# Claude Code session-local harness state (regenerable: lane queue, branch lock)
.claude/state/

# Graph receipt artifacts (regenerable per-commit)
state/artifacts/graph_receipts/

# Cloned reference repos (research, not dependency)
opentelemetry-python/

# Homebrew formula (not part of project)
tesseract.rb

# === S213 DATA ARTIFACTS (2026-02-20) ===

# One-off query/analysis exports (regenerable)
cohesion.json
evidence?edges.json
neo4j_query_table_data*.json

# Node package artifacts — historically not a Node project, but filing-ui
# subdirectory is an exception and must be tracked.
package.json
package-lock.json
!filing-ui/package.json
!filing-ui/package-lock.json
!services/temporal/webhook-receiver/package.json
# saas/ monorepo (storefront + workspace packages) IS a Node project — track its manifests.
!saas/package.json
!saas/package-lock.json
!saas/apps/*/package.json
!saas/packages/*/package.json
# storefront static assets (global *.svg rule at L133 would swallow them)
!saas/apps/*/public/**

# === RENAME MIGRATION CLEANUP (2026-02-22) ===

# Untracked directories with user content
React Diagrams/
.thesrc/
cli/
journey/
CLAUDE 2.md
README 2.md
*.docx

# === STRUCTURE CONSOLIDATION (2026-02-22) ===

# Prevent root-level file pollution (use proper directories)
/*.csv
/*.jsonl
/*.tar.gz
/*.pdf
/*.png
/*.plist
/*.jsx

# Root-level files removed from git (git rm --cached)
/CHANGELOG.md
/README_NEW.md
/README\ (4).md
/guardrails.json
/manifestation_map_actions.json
/thesrc_monitor.py
/n8n_templates/

# Screenshots in code dirs
core/audit/*.png

# Old directory names (consolidated into docs/archive/)
/architecture audit/
/handoff-feb4/
/labor day/
/dashboard/
/evidence/
/state/artifacts/*
!/state/artifacts/*.md
/reconcile all/
/thriven_n8n_pack/
/thriven_os.egg-info/

# Compiled Go binaries in cmd/
cmd/thriven-hud/thriven-hud
cmd/thesrc-hud/thesrc-hud

# === WORKER CONSOLIDATION (2026-02-22) ===

# Old top-level dirs (merged into workers/)
/layer3/
/thesrc-hud/
gpt-oss-120b/
.gitnexus
supabase/.env.local
gitnexus
knowledge-graph-agent/
agents/ingest/external/_clones/

# Archived content (taxonomy consolidation)
state/data/vendored/

# Untracked directories (taxonomy cleanup S2026-03-16)
knowledge-graph-agent/
logs/
.cache/
.wrangler/
thesrc.egg-info/
thriven-BACKUP/

# === TAXONOMY WAVE A (2026-03-17) ===
# Regenerable cached web pages (888 files, 7MB)
agents/webfetch/docs/fetched/
# Regenerable insight/analysis results
agents/*/docs/insights/
agents/*/docs/results/
# Graph receipt artifacts (already covered by state/artifacts/)
agents/artifacts/graph_receipts/
# Agent archive dirs (superseded content)
agents/*/docs/archive/
# Claude worktree debris
.claude/worktrees/
state/data/bio/structures/*.cif

# Session state — local only, causes git slowness (H-14)
state/memory/session_archives/
state/memory/session_outputs/
state/memory/session_distillations/
state/memory/active_plan.json
state/memory/CONTINUATION.json
state/memory/CONTINUATION.md
state/data/bio/bulk/
data/
alphagenome/
bulk/
bindingdb_compounds.json
download_summary.json
docs/ingested/semantic-scholar-api/*.json
docs/ingested/openalex-api/*.csv
docs/ingested/papers/arxiv_*.pdf

# obrain ONNX models (binary, not tracked)
models/obrain/*.onnx
models/obrain/semantic-compressor/*.onnx
# domain-projection torch checkpoints (6MB each binary; the *.stub.json sibling is the tracked pointer)
models/domain_projection/*.pt
aura-cli/
.venv-filing/
obscura
ghostty/

# S2026-05-21: large transient operational checkpoints — removed from history via
# git filter-repo + guarded by scripts/precommit_large_file_guard.py (exceeded GitHub 100MB).
state/candidates/knn_l2_candidates.jsonl
state/candidates/batches/_deadletter.jsonl
state/candidates/**/*.jsonl

# S2026-06-07: defense-in-depth against the artifact-sync materializing a vault
# pointer (file_path `VAULT://…`) as a committable plaintext secret. The sync
# (scripts/sync_artifacts_from_pg.py) now refuses such paths at the source, but
# never let a `VAULT:`-shaped path enter git even if a host runs an old build.
VAULT:
VAULT:/
/VAULT:*

# S2026-06-16 secret-leak hardening (workflow finding): env-backup + .bak- evasions
*.env.backup*
macmini.env.*
*.env.*
*.bak-*

# regenerable model-intelligence snapshots (collector reproduces on demand)
state/ops/MODEL_INTELLIGENCE_*.json
state/ops/MODEL_INTELLIGENCE_*.md

# host-specific virtualenv — never track (landed in main as a broken /Users/susieatlas symlink, fixed S2026-06-24)
.venv
.venv/

# S2026-06-25 git-hygiene: stray clones / sample templates / eval temp (0 tracked files).
# These would catastrophically bloat the repo (22k+ junk files) on any `git add -A`. Not project source.
money-transfer-project-template-ts/
cloudflare-cli/
external/_clones/
.eval-tmp/
scratchpad/

# === S2026-06-30 git-hygiene closure ===
# Repo HISTORY is clean (0 tracked files >5MB). The bloat below is untracked-on-disk only and
# (a) makes `git status` noisy, (b) blocks pushes at GitHub's 2 GiB pack wall, (c) risks staging PII.
# Forward-ignore so `git add -A` can NEVER stage data/media/PII again.
# Alt-therapies source media (~1.4G: PDFs, video course, manuals, scanned sources)
alt-therapies/
# Personal genomic data (PII — AncestryDNA VCFs etc.) — overrides the !state/data/bio/ re-include above
*.vcf
state/data/bio/vcf/
state/data/bio/bulk/
state/data/bio/usda/
state/data/bio/gwas/
# Bulk scientific data dumps (regenerable from source / object storage)
/bulk/
data/bulk/
state/data/bulk/
state/exports/
# Stray node_modules across app subdirs + native binaries
**/node_modules/
*.node
# Large archive / db blobs (regenerable)
*.tar.gz
*.bz2
*.sqlite
*.sqlite3
filing-ui/out/
# Session scratch files
scratchpad_*.py
pine/research/.price_cache/

# Raw local session-transcript exports (109MB+ JSONL) — archive off-repo; scrolls (.md) may be committed
state/chat_transcripts/local/
