Fix/user reported issues -> 2.6.2

.claude/feature-requests-v2.6.3/mad-zero-investigation.md

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+# MAD=0 investigation — awaiting data from scientists
+
+**Reported by**: scientists (EK-march-2026)
+**Priority**: bug (unresolved)
+**Complexity**: unknown — need more information
+
+## Problem
+
+PCA MAD calculation returns 0.0 for some data. Root cause is unclear — the initial `|| 0` → `isFinite` guard did not address the real issue.
+
+## Status
+
+Request sent to scientists (2026-03-29) asking for:
+1. Direct comparisons between PMTools and software where MAD is calculated correctly
+2. The formula they expect for PCA and PCA0 MAD calculation
+3. More data files and step ranges showing discrepancies
+
+## Technical notes
+
+- The `|| 0` fallback in PCA was replaced with an `isFinite` guard, but this is a defensive fix, not a root-cause fix.
+- Relevant code: `src/utils/statistics/calculation/calculatePCA_pmd.ts`
+- Cannot proceed without reference data or expected formulas from scientists.

.claude/feature-requests-v2.6.3/merge-pmm-files.md

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+# Merge multiple PMM files (append collections)
+
+**Requested by**: Ekaterina Kulakova (EK-march-2026, issue #2)
+**Priority**: feature request
+**Complexity**: medium
+
+## Problem
+
+Importing a new file replaces the previously loaded data. Users who have interpretation results split across multiple PMM files (e.g., different field seasons or labs) cannot combine them without external tools.
+
+## Desired behavior
+
+Users should be able to either:
+1. Select multiple PMM files at once (Ctrl+click / Shift+click in the file dialog), or
+2. Use an "Add to results" / "Append" option that imports a file without clearing existing data.
+
+## Technical notes
+
+- The file upload pipeline currently replaces the Redux store with new data on each import.
+- Need to modify the import flow to support an "append" mode alongside "replace" mode.
+- UI options: a toggle/checkbox in the upload dialog, or a separate "Add files" button next to the existing "Open files" button.
+- Must handle potential ID/label collisions when merging collections.

.claude/feature-requests-v2.6.3/multi-window-support.md

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+# Multi-window / multi-collection support
+
+**Requested by**: Roman Veselovsky (RV-march-2026, issue #1)
+**Priority**: feature request
+**Complexity**: large
+
+## Problem
+
+All browser tabs/windows share the same Redux state via localStorage. Opening PMTools in a new tab mirrors the first tab's data. Users cannot view different collections side by side.
+
+## Desired behavior
+
+Users should be able to open multiple PMTools instances (tabs or windows) and work with independent collections in each.
+
+## Technical notes
+
+- Current architecture persists Redux state to localStorage, which is shared across all tabs of the same origin.
+- Possible approaches:
+  1. **sessionStorage** — scoped per tab, simplest migration but breaks "reopen tab" persistence.
+  2. **URL-based state** — encode collection ID in the URL; each tab loads its own data.
+  3. **Per-tab ID** — generate a unique tab ID on load, key localStorage entries by tab ID.
+- This is a fundamental architecture change — needs careful design to avoid breaking existing single-tab workflows.

.claude/feature-requests-v2.6.3/vgp-both-coordinate-systems.md

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+# VGP for both geographic and stratigraphic coordinate systems
+
+**Requested by**: Alexander Pasenko (AP-march-2026, issue #2)
+**Priority**: major improvement
+**Complexity**: medium
+
+## Problem
+
+VGP calculations currently use whichever coordinate system is selected (geographic OR stratigraphic). Users need VGP computed and displayed for both systems simultaneously, similar to how PCA shows Dgeo/Igeo and Dstrat/Istrat side by side.
+
+## Desired behavior
+
+1. VGP table and graph should show poles for both geographic and stratigraphic coordinate systems at the same time.
+2. (Stretch) Allow users to input custom directions directly in the VGP section and calculate VGP without importing a DIR file — currently requires an external tool like Excel.
+
+## Technical notes
+
+- Key files:
+  - `src/components/AppLogic/DataTablesDIR/SitesDataTable/SitesDataTable.tsx` — lines 128–130 select one coord system
+  - `src/utils/statistics/calculation/calculateVGP.ts` — pure VGP math
+  - `src/components/AppLogic/VGP/` — VGP display components
+  - `src/utils/GlobalTypes.ts` — VGPData type definition
+- Current behavior: VGP uses either `DgeoFinal/IgeoFinal` or `DstratFinal/IstratFinal` based on the `reference` toggle. VGPData stores a single set of pole coordinates.
+- Suggested approach: extend VGPData to include both `poleLatGeo/poleLonGeo` and `poleLatStrat/poleLonStrat`. Calculate VGP for both systems when site data is processed.

.claude/skills/autoplan/SKILL.md

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+/Users/i1948374/PMTools_2.0/.claude/skills/gstack/autoplan/SKILL.md

.claude/skills/benchmark/SKILL.md

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+/Users/i1948374/PMTools_2.0/.claude/skills/gstack/benchmark/SKILL.md

.claude/skills/browse/SKILL.md

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+/Users/i1948374/PMTools_2.0/.claude/skills/gstack/browse/SKILL.md

.claude/skills/canary/SKILL.md

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+/Users/i1948374/PMTools_2.0/.claude/skills/gstack/canary/SKILL.md

.claude/skills/careful/SKILL.md

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+/Users/i1948374/PMTools_2.0/.claude/skills/gstack/careful/SKILL.md

.claude/skills/checkpoint/SKILL.md

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+/Users/i1948374/PMTools_2.0/.claude/skills/gstack/checkpoint/SKILL.md

.claude/skills/codex/SKILL.md

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+/Users/i1948374/PMTools_2.0/.claude/skills/gstack/codex/SKILL.md

.claude/skills/connect-chrome/SKILL.md

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+/Users/i1948374/PMTools_2.0/.claude/skills/gstack/connect-chrome/SKILL.md

.claude/skills/cso/SKILL.md

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+/Users/i1948374/PMTools_2.0/.claude/skills/gstack/cso/SKILL.md

.claude/skills/design-consultation/SKILL.md

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+/Users/i1948374/PMTools_2.0/.claude/skills/gstack/design-consultation/SKILL.md

.claude/skills/design-html/SKILL.md

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+/Users/i1948374/PMTools_2.0/.claude/skills/gstack/design-html/SKILL.md

.claude/skills/design-review/SKILL.md

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+/Users/i1948374/PMTools_2.0/.claude/skills/gstack/design-review/SKILL.md

.claude/skills/design-shotgun/SKILL.md

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+/Users/i1948374/PMTools_2.0/.claude/skills/gstack/design-shotgun/SKILL.md

.claude/skills/devex-review/SKILL.md

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+/Users/i1948374/PMTools_2.0/.claude/skills/gstack/devex-review/SKILL.md

.claude/skills/document-release/SKILL.md

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+/Users/i1948374/PMTools_2.0/.claude/skills/gstack/document-release/SKILL.md

.claude/skills/freeze/SKILL.md

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+/Users/i1948374/PMTools_2.0/.claude/skills/gstack/freeze/SKILL.md

.claude/skills/gstack-upgrade/SKILL.md

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+/Users/i1948374/PMTools_2.0/.claude/skills/gstack/gstack-upgrade/SKILL.md

.claude/skills/gstack/.env.example

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+# Copy to .env and fill in values
+# bun auto-loads .env — no dotenv needed
+
+# Required for LLM-as-judge evals (bun run test:eval)
+ANTHROPIC_API_KEY=sk-ant-your-key-here

.claude/skills/gstack/.github/actionlint.yaml

@@ -0,0 +1,4 @@
+self-hosted-runner:
+  labels:
+    - ubicloud-standard-2
+    - ubicloud-standard-8

.claude/skills/gstack/.github/docker/Dockerfile.ci

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+# gstack CI eval runner — pre-baked toolchain + deps
+# Rebuild weekly via ci-image.yml, on Dockerfile changes, or on lockfile changes
+FROM ubuntu:24.04
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+# System deps
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    git curl unzip ca-certificates jq bc gpg \
+    && rm -rf /var/lib/apt/lists/*
+
+# GitHub CLI
+RUN curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg \
+    | gpg --dearmor -o /usr/share/keyrings/githubcli-archive-keyring.gpg \
+    && echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" \
+    | tee /etc/apt/sources.list.d/github-cli.list > /dev/null \
+    && apt-get update && apt-get install -y --no-install-recommends gh \
+    && rm -rf /var/lib/apt/lists/*
+
+# Node.js 22 LTS (needed for claude CLI)
+RUN curl -fsSL https://deb.nodesource.com/setup_22.x | bash - \
+    && apt-get install -y --no-install-recommends nodejs \
+    && rm -rf /var/lib/apt/lists/*
+
+# Bun (install to /usr/local so non-root users can access it)
+ENV BUN_INSTALL="/usr/local"
+RUN curl -fsSL https://bun.sh/install | BUN_VERSION=1.3.10 bash
+
+# Claude CLI
+RUN npm i -g @anthropic-ai/claude-code
+
+# Playwright system deps (Chromium) — needed for browse E2E tests
+RUN npx playwright install-deps chromium
+
+# Pre-install dependencies (cached layer — only rebuilds when package.json changes)
+COPY package.json /workspace/
+WORKDIR /workspace
+RUN bun install && rm -rf /tmp/*
+
+# Install Playwright Chromium to a shared location accessible by all users
+ENV PLAYWRIGHT_BROWSERS_PATH=/opt/playwright-browsers
+RUN npx playwright install chromium \
+    && chmod -R a+rX /opt/playwright-browsers
+
+# Verify everything works
+RUN bun --version && node --version && claude --version && jq --version && gh --version \
+    && npx playwright --version
+
+# At runtime: checkout overwrites /workspace, but node_modules persists
+# if we move it out of the way and symlink back
+# Save node_modules + package.json snapshot for cache validation at runtime
+RUN mv /workspace/node_modules /opt/node_modules_cache \
+    && cp /workspace/package.json /opt/node_modules_cache/.package.json
+
+# Claude CLI refuses --dangerously-skip-permissions as root.
+# Create a non-root user for eval runs (GH Actions overrides USER, so
+# the workflow must set options.user or use gosu/su-exec at runtime).
+RUN useradd -m -s /bin/bash runner \
+    && chmod -R a+rX /opt/node_modules_cache \
+    && mkdir -p /home/runner/.gstack && chown -R runner:runner /home/runner/.gstack \
+    && chmod 1777 /tmp \
+    && mkdir -p /home/runner/.bun && chown -R runner:runner /home/runner/.bun \
+    && chmod -R 1777 /tmp

.claude/skills/gstack/.github/workflows/actionlint.yml

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+name: Workflow Lint
+on: [push, pull_request]
+jobs:
+  actionlint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: rhysd/actionlint@v1.7.11

.claude/skills/gstack/.github/workflows/ci-image.yml

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+name: Build CI Image
+on:
+  # Rebuild weekly (Monday 6am UTC) to pick up CLI updates
+  schedule:
+    - cron: '0 6 * * 1'
+  # Rebuild on Dockerfile or lockfile changes
+  push:
+    branches: [main]
+    paths:
+      - '.github/docker/Dockerfile.ci'
+      - 'package.json'
+  # Manual trigger
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubicloud-standard-2
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - uses: actions/checkout@v4
+
+      # Copy lockfile + package.json into Docker build context
+      - run: cp package.json .github/docker/
+
+      - uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: docker/build-push-action@v6
+        with:
+          context: .github/docker
+          file: .github/docker/Dockerfile.ci
+          push: true
+          tags: |
+            ghcr.io/${{ github.repository }}/ci:latest
+            ghcr.io/${{ github.repository }}/ci:${{ github.sha }}

.claude/skills/gstack/.github/workflows/evals-periodic.yml

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+name: Periodic Evals
+on:
+  schedule:
+    - cron: '0 6 * * 1'  # Monday 6 AM UTC
+  workflow_dispatch:
+
+concurrency:
+  group: evals-periodic
+  cancel-in-progress: true
+
+env:
+  IMAGE: ghcr.io/${{ github.repository }}/ci
+  EVALS_TIER: periodic
+  EVALS_ALL: 1  # Ignore diff — run all periodic tests
+
+jobs:
+  build-image:
+    runs-on: ubicloud-standard-2
+    permissions:
+      contents: read
+      packages: write
+    outputs:
+      image-tag: ${{ steps.meta.outputs.tag }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - id: meta
+        run: echo "tag=${{ env.IMAGE }}:${{ hashFiles('.github/docker/Dockerfile.ci', 'package.json') }}" >> "$GITHUB_OUTPUT"
+
+      - uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Check if image exists
+        id: check
+        run: |
+          if docker manifest inspect ${{ steps.meta.outputs.tag }} > /dev/null 2>&1; then
+            echo "exists=true" >> "$GITHUB_OUTPUT"
+          else
+            echo "exists=false" >> "$GITHUB_OUTPUT"
+          fi
+
+      - if: steps.check.outputs.exists == 'false'
+        run: cp package.json .github/docker/
+
+      - if: steps.check.outputs.exists == 'false'
+        uses: docker/build-push-action@v6
+        with:
+          context: .github/docker
+          file: .github/docker/Dockerfile.ci
+          push: true
+          tags: |
+            ${{ steps.meta.outputs.tag }}
+            ${{ env.IMAGE }}:latest
+
+  evals:
+    runs-on: ubicloud-standard-2
+    needs: build-image
+    container:
+      image: ${{ needs.build-image.outputs.image-tag }}
+      credentials:
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+      options: --user runner
+    timeout-minutes: 25
+    strategy:
+      fail-fast: false
+      matrix:
+        suite:
+          - name: e2e-plan
+            file: test/skill-e2e-plan.test.ts
+          - name: e2e-design
+            file: test/skill-e2e-design.test.ts
+          - name: e2e-qa-bugs
+            file: test/skill-e2e-qa-bugs.test.ts
+          - name: e2e-qa-workflow
+            file: test/skill-e2e-qa-workflow.test.ts
+          - name: e2e-review
+            file: test/skill-e2e-review.test.ts
+          - name: e2e-workflow
+            file: test/skill-e2e-workflow.test.ts
+          - name: e2e-routing
+            file: test/skill-routing-e2e.test.ts
+          - name: e2e-codex
+            file: test/codex-e2e.test.ts
+          - name: e2e-gemini
+            file: test/gemini-e2e.test.ts
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Fix bun temp
+        run: |
+          mkdir -p /home/runner/.cache/bun
+          {
+            echo "BUN_INSTALL_CACHE_DIR=/home/runner/.cache/bun"
+            echo "BUN_TMPDIR=/home/runner/.cache/bun"
+            echo "TMPDIR=/home/runner/.cache"
+          } >> "$GITHUB_ENV"
+
+      - name: Restore deps
+        run: |
+          if [ -d /opt/node_modules_cache ] && diff -q /opt/node_modules_cache/.package.json package.json >/dev/null 2>&1; then
+            ln -s /opt/node_modules_cache node_modules
+          else
+            bun install
+          fi
+
+      - run: bun run build
+
+      - name: Run ${{ matrix.suite.name }}
+        env:
+          ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}
+          OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
+          GEMINI_API_KEY: ${{ secrets.GEMINI_API_KEY }}
+          EVALS_CONCURRENCY: "40"
+          PLAYWRIGHT_BROWSERS_PATH: /opt/playwright-browsers
+        run: EVALS=1 bun test --retry 2 --concurrent --max-concurrency 40 ${{ matrix.suite.file }}
+
+      - name: Upload eval results
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: eval-periodic-${{ matrix.suite.name }}
+          path: ~/.gstack-dev/evals/*.json
+          retention-days: 90