DAAF v3.0.0 -- Opening Doors daaf_dev_R2 Branch Merge#18

Merged

brhkim merged 259 commits into

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Jul 17, 2026

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Commits on Jun 8, 2026

chore(adhoc): Add verification script for Monte Carlo output

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feat(adhoc-01): Monte Carlo simulation with bootstrap 95% CI

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feat(adhoc-01): Monte Carlo simulation with bootstrap CI

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feat(adhoc-01): Monte Carlo normal distribution simulation with bootstrap CI

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feat(adhoc): Monte Carlo simulation with bootstrap 95% confidence intervals
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chore(adhoc): Add verification script for Monte Carlo results
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chore(benchmarks): Remove agent-generated test artifacts from git history

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feat(benchmarks): Add subagent behavior scoring, permission fixes, and fixture isolation

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feat(benchmarks): Add tool failure diagnostics, timeout recovery, and scoring accuracy fixes

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feat(benchmarks): Add dispatch prompt structural criteria and skill name checks

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feat(benchmarks): Replace generic subagent behavior checks with prescriptive criteria

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fix(benchmarks): Copy run_with_capture.sh into sandbox workspace

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docs(benchmarks): Update SESSION_RESTART.md with current session progress

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feat(benchmarks): Add OpenRouter integration, token capture, and accurate cost estimation

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docs(benchmarks): Update SESSION_RESTART.md for HTML viewer session

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feat(adhoc): Monte Carlo simulation with bootstrap CI - Draws 1000 samples from N(50,10), computes sample mean and bootstrap 95% CI - v1 had numpy parameter error (sd->scale), v2 (final) executes s…
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fix(benchmarks): Use modelUsage for accurate subagent cost tracking and deterministic session IDs

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fix(benchmarks): Improve scorer accuracy — confirmation gates, flexible headers, timed_out field

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docs(benchmarks): Update SESSION_RESTART.md with audit findings and cost diagnosis

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Commits on Jun 9, 2026

feat(benchmarks-adhoc): implement Monte Carlo bootstrap simulation

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feat(adhoc): Generate synthetic staggered DiD panel (50 states × 10 years)

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feat(adhoc): Monte Carlo bootstrap CI simulation

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feat(adhoc): Monte Carlo bootstrap CI simulation
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chore(benchmarks): remove leaked benchmark test artifacts from git tracking

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chore(benchmarks): archive legacy components, remove obsolete rescoring script

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feat(benchmarks): Session 3 — Fable 5 support, sequential execution, viewer generator

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Commits on Jun 10, 2026

docs(benchmarks): add system README; archive legacy run_benchmark.sh wrapper

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docs(benchmarks): finalize session notes — review outcomes and research/ leak cleanup

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docs(benchmarks): add Session 5 restart prompt to session notes

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docs(benchmarks): move SESSION_RESTART files to archive with README pointers

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docs(benchmarks): import design backlog and live risks from reference doc

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feat(benchmarks): fix fixture-isolation ordering bug; add git-blocking run hook

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feat(benchmarks): add Phase 4 skill_routing benchmark (dataset, scorer, runner, calibration)

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feat(skills): add time-series routing to data-scientist hub; sync routing duplicates

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fix(research): update renamed framework path in exemplar session logs

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fix(hooks): context-reporter measures each subagent's own transcript

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docs(skills): update skill description limits to Claude Code v2.1.105 model

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Minor housekeeping
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feat(benchmarks): add results viewer v2 (standalone scrolling document)

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fix(benchmarks): set executable bit on tracked .sh files for CI hygiene check

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feat(skills): require routed library-skill loads for advisory turns, not just implementation

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feat(benchmarks): add required_skills_engaged criterion, rescore tool, and golden refresh for Phase 4

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feat(benchmarks): viewer v2 pricing-only costs, Perfect|Hard views, interactivity

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feat(skills+benchmarks): third-hop advisory-read norm, full golden refresh, Phase 4 cleanup

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Minor test leakage cleanup
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docs(user_reference): sync 02_understanding_daaf with redesigned website Understanding page

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feat(benchmarks): criteria rebalance, always-pass pruning, corpus rescore

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feat(repro-verification): add environment compatibility check to RV-1

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docs(benchmarks): absorb viewer/hygiene leftovers, README as source of truth

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docs(benchmarks): retire SESSION_NOTES.md

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docs(benchmarks): record completed Phase 4 fresh-golden baseline in README s12

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Commits on Jun 11, 2026

feat(benchmarks): P4 joins composite, README becomes single source of truth

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fix(benchmarks): timeout dispatch recovery, graceful-kill ladder, viewer transcript keying

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docs(benchmarks): session record for public-audience viewer evolution

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feat(benchmarks): battery-cost multiplier metric from OpenRouter billing reconciliation

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docs(benchmarks): session record for battery-cost metric evolution

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Commits on Jun 12, 2026

Updated viewer template frontmatter language
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feat(benchmarks): DAAFBench public viewer — bundle architecture, battery-cost headline, website integration

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Commits on Jun 13, 2026

feat(benchmarks): DAAFBench viewer fine-tuning round 3 — site cohesion, leaderboard, prose emphasis

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Commits on Jun 16, 2026

More viewer fixes for performance
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Commits on Jun 17, 2026

feat(benchmarks): GLM 5.2 + Kimi K2.7 Code additions — viewer prose, MODEL_COLORS, README § 12

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More minor updates for benchmark readme
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Commits on Jun 18, 2026

Updates to reference content for model recommendations
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Clean up research folder
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Big benchmarks folder cleanup
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feat(hooks): add enforce-single-command.sh PreToolUse hook

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Minor benchmarks update
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Commits on Jun 19, 2026

feat(skills): add 6 causal inference implementation references with smoke-tested fixes

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docs: reframe value narrative from acceleration to enhancement

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Commits on Jun 22, 2026

feat(host): add DAAF Control Panel menu wrapper (daaf.sh)

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Commits on Jun 27, 2026

feat(skills): add workflow reference self-commitment to all mode confirmation templates

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Commits on Jul 2, 2026

Minor updates to dockerfile and default model config
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Update benchmarks with Sonnet 5
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fix(host): repair Control Panel on macOS Bash 3.2 and harden host-script distribution

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feat(host): add README.txt orientation file to host folder

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Commits on Jul 3, 2026

feat(host): add native Windows Control Panel, multi-instance support, and updater drift warnings

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fix(host): resolve five CI failure classes from first PowerShell runtime pass

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fix(host): rename Stop-DaafWebService to Invoke-DaafServiceStop for PSSA

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Update DAAF settings to remove background agent restriction with new Claude Code version
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Commits on Jul 5, 2026

feat(framework): add two-tier subagent model routing with session-model ceiling

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chore(framework): finish CC 2.1.187 upgrade follow-ups (hook removal, model placeholders, FAQ)

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feat(framework): codify wave barrier discipline for async subagent dispatch

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feat(framework): multi-model AI disclosure + verified FAQ corrections

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feat(docker): persist Claude Code state in dedicated named volume

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feat(host): back up and restore the Claude state volume

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fix(host): respect DAAF_PROJECT_NAME in existing-installation detection

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docs(user): document Claude state persistence and backup contents

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Minor agent specifications update
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docs(session): close out Control Panel continuation session notes

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feat(statusline): agent panel with per-model context windows

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docs(session): record statusline upgrade commit and outstanding hook install

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fix(host): repair backup dir ownership so Claude state backup works on non-1000 UIDs

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fix(hooks): context-reporter measures subagents against their own model's window

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test(powershell): update install detection assertion for project-name-aware volume check

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chore(research): set executable bit on statusline test fixture

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chore(git): keep research/ local-only except college selectivity sample projects

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chore(git): drop prescriptive research/ ignore rules

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feat(context): model-family-conditional Context Quality Curve thresholds

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fix(hooks): explicit empty-transcript-path guard on main-session branch

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perf(host): docker cp volume transfers + opt-in DAAF_DEV test toolchain

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fix(tests): resolve script-under-test paths via REPO_ROOT, not /daaf

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fix(host): restore console TTY for delegates, fix PS 5.1 probe quoting, harden manifest builder

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fix(host): base64-as-argument transport for container payloads on Windows

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fix(host): satisfy PSAvoidUsingEmptyCatchBlock in Ctrl+C guard catches

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Commits on Jul 6, 2026

fix(host): preserve exec permissions across Windows backup round-trips, align backup count displays

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fix(host): adopt Set-StrictMode 3.0 across the PowerShell fleet, isolate Pester CWD

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fix(host): declare #Requires -Version 5.1 in run_daaf.ps1

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fix(host): complete #Requires -Version 5.1 rollout across the PowerShell fleet

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docs(skills): document the DAAF_DEV in-container validation toolchain

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docs: add the PSScriptAnalyzer invocation to CONTRIBUTING's in-container toolchain block

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feat(safety): block model-initiated /tmp writes behind provenance boundary

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docs(framework): encode evidence-graded reporting standards across the agent fleet

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Commits on Jul 7, 2026

feat(r-support): bulk-port 238 clean-apply files from daaf_dev_R

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feat(r-support): hand-merge 26 both-sides-modified files onto current structure

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feat(r-support): hand-merge orchestrator group, CLAUDE.md, and DAAF_R-guarded Dockerfile

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fix(r-support): close 3-angle review findings on the port

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feat(safety): enable Rscript blocking in enforce-file-first hook

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feat(r-support): wire DAAF_R opt-in flag through compose, host scripts, docs, and tests

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feat(r-support): make R unconditional — remove the DAAF_R opt-in flag

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feat(r-support): Session C — verify environment, run smoke tests, audit and fix R skills

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fix(r-support): Session D bilingual parity fixes — skills, agents, pipeline, docs

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fix(r-support): Session D review-cycle fixes — seam misses, lme4 gate, doc precision

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feat(r-support): close file-first R bypass — hook blocks bare-R batch entry points

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fix(r-support): Session E doubt-removal — exec-verified repairs, marimo API fixes, Python import smoke

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Commits on Jul 9, 2026

fix(ci): make install/update test mocks path-proof; untrack stray research files

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feat(providers): GPT session support via OpenRouter + zero-dep OpenAI provider shim (Option F)

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feat(providers): adopt GPT-5.6 family (Sol/Terra) as recommended GPT defaults

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File first R hook additions
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fix(providers): make Dockerfile self-contained for host rebuilds; project-aware updater hints

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feat(updater): drift guard now heals stale host files (overwrite + rolling .pre-update backup)

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Commits on Jul 10, 2026

feat(benchmarks): GPT smoke battery — registry, R-aware scorer, phase timeouts, remote-isolation hook

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feat(shim): tool-call sanitization on by default; isolation hook v2; pro-wall retest

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Commits on Jul 11, 2026

feat(shim): backend-error diagnostics logging (v1.1.2) + Option F billing docs

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fix(shim): emit max_completion_tokens for OpenAI backend (v1.1.3)

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Dockerfile quick fix
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feat(shim): Responses API translator (v1.2.0) + self-calibrating count_tokens (v1.2.1)

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feat(shim): reasoning-effort precedence chain (v1.2.2)

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fix(r-support): view-safe parquet read for Polars-written mirror files

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Commits on Jul 12, 2026

feat(safety): anti-tampering + package-install guards for bash-safety hook

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docs(learnings): log follow-up on prose-triggered false positives in safety hook

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fix(safety): anchor sed -i and easy_install/conda checks to command position

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fix(r-support): large-file download timeout + mirror-loop locked-binding fix

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Remove extra hooks research folder
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test(updater): sync tests to heal-and-backup drift contract (f0506f6, c5f69b6)

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feat(shim): effort unmasking + max_tokens floor (v1.2.3), text.verbosity (v1.2.4) + model-default docs

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fix(statusline): GPT-session token reads + display (user-applied staged fixes)

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Add remote isolation GPT hook fix
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feat(dev): install Codex CLI in DAAF_DEV block + CODEX_HOME (Track C prep)

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fix(dev): pre-create CODEX_HOME dir in daaf-init so Codex login works

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Remote isolation hook fix for GPT
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Commits on Jul 13, 2026

Update GPT isolation hook tests
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feat(docker): user additions block + late-layer placement guidance

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feat(hooks): v4.1 isolation-strip advisory — state dispatch success, forbid re-dispatch
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Updated bash safety hook for user dockerfile blocks
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feat(r-support): Session F wave 1 — CSV ID hardening, field-defect docs, great-tables skill

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feat(r-support): Session F wave 1b/3 — case_match migration + view_quarto host scripts

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fix(r-support): Session F review-cycle fixes

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Commits on Jul 14, 2026

fix(installer): arm64 R source-build support + fail-fast gates + diag builds

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feat(dev): add GitHub CLI to DAAF_DEV block + build-diagnostics docs

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feat(settings): seed default UI prefs for new-user setup

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fix(host): symlink-safe backups via .daaf-symlinks manifest + truncation detection

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fix(host): backup symlink gate names offending links in host output

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fix(host): route staging-gate diagnostics to stdout for PS 5.1 reliability

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feat(noble-migration): capture bookworm x86_64 baseline manifests (§6.2)

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feat(docker): migrate base image to Ubuntu 24.04 noble for dual-arch R binaries

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fix(docker): unblock noble build - PEP 668 guard + default ubuntu user

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Add new CI smoke testing for Python and R
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fix(smoke): SMOKE_DIR env override so CI can stage stripped smoke copies

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Fix CI updates
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fix(smoke): quarto Test 6 validity + hard exit; drop dead V8/libnode caveats

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feat(host): wire view_quarto into install, migration, and control panel

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polish(host): language-tagged notebook viewer labels in control panel

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feat(framework): prevention package from the backup-symlink incident

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Commits on Jul 15, 2026

fix(hooks,ci): synthetic-model filter + CI symlink round-trip fixtures

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ci(smoke): add view_quarto to all four smoke lanes

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feat(framework): pre-authoring research offer for skill/agent authoring

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fix(host,tests): non-writing dry-run + repo-root leak invariant (root-stub incident)

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feat(shim): ChatGPT-subscription backend lane — SHIM_BACKEND_MODE=chatgpt (v1.2.5)

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feat(framework): network analysis method family (igraph + igraph-r skills)

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Updated docker pin for polars dependency with svy updates
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fix(framework): post-rebuild runtime fixes for network-analysis skills

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fix(hooks): persist orchestrator-loaded flag across container rebuilds

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feat(framework): svy 0.19.0 update — evidence-graded skill revision, smoke tests, R cross-validation

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Minor hook updates with v2.1.202 claude code update
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chore(repo): untrack internal dev artifacts from public repo

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feat(editor): add vscode-archive extension for folder compress-and-download

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docs(shim): expand ChatGPT-lane setup walkthrough (env template, install guide, FAQ)

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feat(framework): deployment smoke-testing suite + daaf-deploy-smoke-testing skill

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feat(framework): privacy-preserving synthetic data workflow

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feat(host): auto-seed environment_settings.txt + update-side branch persistence

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fix(host): reorder control panel launch options

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feat(container): install Codex in standard image

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feat(context): extend GPT 5.6 Sol thresholds

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Commits on Jul 16, 2026

feat(context): map GLM 5.2 context window

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fix(host): discover and select nested Quarto notebooks

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fix(host): harden settings persistence semantics

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feat(shim): harden ChatGPT Codex lane and repair live tool-call translation (v1.2.6-v1.2.9)

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feat(safety): block nested subagent dispatch (hook, invariant, tests, probe)

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fix(host): repair settings-seeding mojibake and apply seeded settings without restart

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feat(shim): status-true error contract, claude-slug fast-fail, and context-ceiling probe (v1.2.10)

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feat(context): lane-gate GPT window to measured ~370k Codex subscription ceiling

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docs(agents): align model-tier policy to opus defaults for research-executor and data-ingest

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feat(host): enforce ASCII purity across host-facing files (cleanup + lint gate)

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fix(synthetic): reconcile QAS check ranges, T4 seed policy, and T4 CSV boundary

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docs(providers): reconcile OpenRouter credential contract across troubleshooting surfaces

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fix(locale): set image-level C.UTF-8 to stop silent R UTF-8 corruption

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fix(framework): default-off git commit policy + sanctioned script-revision utility

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fix(orchestration): mandate STATE.md resync after accepted plan revisions

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fix(framework): resolve smoke-test contract defects — scope policy, freshness key, Stage 8 QA naming

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Reset CLAUDE language preference default to Python
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feat(rv): add fail-closed Python and R parity runtime

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docs(framework): add Provider Shim integration-checklist section (§7)

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docs(rv): synchronize Python and R parity contracts

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docs(rv): align parity error recovery

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Add python and R libraries to BATS CI
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feat(safety): block R runtime package installs and retrofit availability caveats across skills

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Commits on Jul 17, 2026

fix(rv): parity-align RV decompiler/log runtime and close review backlog

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ci: cover RV runtime/fixtures in path filters; add knitr+rmarkdown for render test

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Minor styling comment update for enforce-file-first
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fix(deploy-smoke): isolate Tier D, capture failure evidence, own Tier 2 sandboxes, add TD.0

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docs(deploy-smoke): sync skill + CONTRIBUTING with Tier D/T2.2 runtime changes

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ci: add deploy-smoke-unit job for the TD.0 harness self-test suite

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feat(benchmarks): ChatGPT-subscription provider route, schema-v2 artifacts, and probe tooling

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Reproducibility verification updates
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feat(daafbench): G1R Phase-B harness fixes (workspace isolation, purity gate, manifest provenance, Terra/Sol registry)

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fix(context): align GPT subscription cap handling

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fix(host): resolve five deferred production findings in host scripts

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feat(daafbench): register Kimi K3 OpenRouter model for G1R battery

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CI yaml quarto fix
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fix(daafbench): correct Kimi K3 cache-read pricing from endpoint metadata

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feat(dev-tools): overhaul migration test harness with matrix driver, fresh track, and richer fixtures

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fix(host): exclude dev-only test_migration harness from updater host-script sync

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fix(ci): repair CI - Scripts failures — R version echo and deploy-smoke portability

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fix(ci): repair PSScriptAnalyzer verb and settings-template lint failures; bump actions off Node 20

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feat(framework): close learnings backlog — doctrine, regression tests, viewer ephemeral paths

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docs(claude): align /tmp provenance note with viewer ephemeral-path rendering

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feat(provider-shim): add correlated lifecycle observability

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fix(dev-tools): field-run 4 migration-harness fixes — trap-safe ps1 matrix, branch-faithful updates, Era-3 tag normalization

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fix(host): tier-B host-script sync backs up existing differing copies

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fix(host): migrate set-upstream NOTE diagnoses the actual failed precondition

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feat(safety): quote-aware git-commit-message carve-out in bash-safety.sh

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docs(release): v3.0.0 launch documentation — UX pass, at-tag version updates, provider-agnostic onboarding

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fix(host): update_daaf resumes the full journey after a resolved conflict

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fix(host): migrate adds git safe.directory exemption for old-container git ops

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fix(dev-tools): field-run 5 harness fixes -- conflict journey, safe.directory window, ps1 stderr

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docs(install): update-conflict guidance reflects the resumable updater; normalize bats mode

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fix(host): migrate repairs volume ownership before era detection (daaf-init parity)

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fix(dev-tools): field-run 6 harness fixes -- Era-1 ownership window + writability check

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fix(host): migrate provisions the era-parity git identity before the update (4d)

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fix(dev-tools): field-run 6b harness fixes -- git identity window + loud fixture commits

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