fix: plain clone works fully + Deno container (Refs affinescript#122)

## Make a plain clone work fully + Deno container (Refs
affinescript#122, #126; ubicity#30)

Follow-up to #31. After the `.ts` elimination the repo did not run from
a clean clone. This makes it work end-to-end, including containerised.

### Fixes

1. **`src/storage.js` regenerated** with the fixed async-IIFE backend
   (affinescript#126). The version merged in #31 was generated *before*
   that fix, so `loadAllExperiences` was a `SyntaxError`
   (`await` inside a non-async IIFE).
2. **`deno.json`**: `exports` → `./src/index.js`; added
   `"nodeModulesDir": "auto"` (npm:zod had no resolution); every task /
   glob `.ts` entrypoint (`cli`/`capture`/`visualize`/`index`) → `.js`
   (they were deleted in #31).
3. **`node:` prefix** on all bare node-builtin imports deno rejects:
   `export/import` (`fs`), `capture` (`process`, `readline/promises`),
   `mapper/privacy` (`crypto`), `performance` (`perf_hooks`).
4. **`.tool-versions`**: pin `deno 2.7.14` (matches CI `setup-deno`
   and `flake.nix`) so an `asdf`/`mise` clone provisions deno.
5. **Containerfile** rewritten on `denoland/deno:2.7.14` (was a stale
   Node image that cannot run this Deno project); `.dockerignore`
   keeps `tests/` so the image can run the suite; `docker-compose.yml`
   names `Containerfile` explicitly so `docker compose` (not just
   podman) finds it.

### Verification

- Local: `deno task test` → **44 passed / 0 failed**.
- Containerised: `docker build -f Containerfile -t ubicity .` → builds
  clean; `docker run --rm ubicity test --allow-read --allow-write
  tests/` → **44 passed / 0 failed**; default CMD (CLI help) works.
- A plain `git clone` now works fully via: host deno (`.tool-versions`
  / `flake.nix` both provide 2.7.14) **or** the container.

`flake.nix` already provided deno (unchanged). storage.affine remains
the source of truth for storage.js (affinescript#122 showcase).

Refs hyperpolymath/affinescript#122 #126, ubicity#30.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Author: hyperpolymath

.dockerignore

@@ -2,13 +2,13 @@ node_modules
 npm-debug.log
 .git
 .gitignore
-*.md
-!README.md
-tests
 .github
 .eslintrc.json
 .prettierrc.json
 ubicity-data/*
 !ubicity-data/.gitkeep
 DENO_MIGRATION_PREVIEW.md
 STACK_ANALYSIS.md
+bin
+coverage
+wasm/target

.tool-versions

@@ -1,2 +1,3 @@
+deno 2.7.14
 nodejs 25.6.1
 just 1.36.0

Containerfile

@@ -1,34 +1,38 @@
-# UbiCity Docker Container
-# Provides isolated environment for running UbiCity tools
+# UbiCity container — Deno runtime.
+#
+# This project is Deno-first (deno.json tasks, Deno.* filesystem APIs,
+# jsr:@std/* + npm: deps). The previous Node Containerfile could not run
+# it. Pinned to the .tool-versions deno so a plain `git clone` builds an
+# image that runs the full test suite and CLI with no host toolchain.
+#
+#   docker build -t ubicity .
+#   docker run --rm ubicity                       # CLI help
+#   docker run --rm ubicity deno task stats
+#   docker run --rm -v ./data:/app/ubicity-data ubicity deno task report
+#   docker run --rm ubicity \
+#     deno test --allow-read --allow-write tests/  # full suite (44 tests)
+FROM denoland/deno:2.7.14
 
-FROM node:20-alpine
-
-# Set working directory
 WORKDIR /app
 
-# Install dependencies
-COPY package*.json ./
-RUN npm ci --only=production
+# Manifests first for build-cache friendliness.
+COPY deno.json deno.lock package.json ./
 
-# Copy application code
-COPY src/ ./src/
-COPY schema/ ./schema/
-COPY examples/ ./examples/
-COPY scripts/ ./scripts/
+# Application + tests + assets (.dockerignore trims git/node_modules/etc).
+COPY . .
 
-# Create data directory
-RUN mkdir -p ubicity-data/experiences ubicity-data/analyses ubicity-data/maps
+# Warm the module cache: jsr:@std/* + npm: deps. nodeModulesDir "auto"
+# in deno.json materialises node_modules at build time so runtime needs
+# no network.
+RUN deno cache src/index.js
 
-# Expose volume for data persistence
+# Data directory (mountable volume for persistence).
+RUN mkdir -p ubicity-data/experiences ubicity-data/analyses ubicity-data/maps
 VOLUME ["/app/ubicity-data"]
 
-# Set Node.js environment
-ENV NODE_ENV=production
-
-# Default command: show help
-CMD ["node", "src/cli.js", "help"]
+ENV UBICITY_LOG_LEVEL=info
 
-# Example usage:
-# docker build -t ubicity .
-# docker run -v ./data:/app/ubicity-data ubicity stats
-# docker run -v ./data:/app/ubicity-data ubicity report
+# Default: CLI help. Override the args to run any deno task / test, e.g.
+#   docker run --rm ubicity test --allow-read --allow-write tests/
+ENTRYPOINT ["deno"]
+CMD ["run", "--allow-read", "--allow-write", "src/cli.js", "help"]

deno.json

@@ -1,28 +1,29 @@
 {
   "name": "@ubicity/core",
   "version": "0.3.0",
-  "exports": "./src/index.ts",
+  "exports": "./src/index.js",
+  "nodeModulesDir": "auto",
   "tasks": {
-    "dev": "deno run --watch src/cli.ts",
-    "start": "deno run --allow-read --allow-write src/cli.ts",
-    "capture": "deno run --allow-read --allow-write src/capture.ts",
-    "capture:quick": "deno run --allow-read --allow-write src/capture.ts quick",
-    "capture:full": "deno run --allow-read --allow-write src/capture.ts full",
-    "visualize": "deno run --allow-read --allow-write src/visualize.ts",
-    "report": "deno run --allow-read --allow-write src/cli.ts report",
-    "hotspots": "deno run --allow-read --allow-write src/cli.ts hotspots",
-    "stats": "deno run --allow-read --allow-write src/cli.ts stats",
+    "dev": "deno run --watch src/cli.js",
+    "start": "deno run --allow-read --allow-write src/cli.js",
+    "capture": "deno run --allow-read --allow-write src/capture.js",
+    "capture:quick": "deno run --allow-read --allow-write src/capture.js quick",
+    "capture:full": "deno run --allow-read --allow-write src/capture.js full",
+    "visualize": "deno run --allow-read --allow-write src/visualize.js",
+    "report": "deno run --allow-read --allow-write src/cli.js report",
+    "hotspots": "deno run --allow-read --allow-write src/cli.js hotspots",
+    "stats": "deno run --allow-read --allow-write src/cli.js stats",
     "test": "deno test --allow-read --allow-write tests/",
     "test:watch": "deno test --watch --allow-read --allow-write tests/",
     "bench": "deno bench --allow-read --allow-write benchmarks/",
-    "check": "deno check src/**/*.ts",
+    "check": "deno check src/**/*.js",
     "fmt": "deno fmt",
     "fmt:check": "deno fmt --check",
     "lint": "deno lint",
-    "cache": "deno cache --reload src/index.ts",
+    "cache": "deno cache --reload src/index.js",
     "compile": "deno task compile:cli && deno task compile:capture && deno task compile:wasm",
-    "compile:cli": "deno compile --allow-read --allow-write --output ./bin/ubicity src/cli.ts",
-    "compile:capture": "deno compile --allow-read --allow-write --output ./bin/ubicity-capture src/capture.ts",
+    "compile:cli": "deno compile --allow-read --allow-write --output ./bin/ubicity src/cli.js",
+    "compile:capture": "deno compile --allow-read --allow-write --output ./bin/ubicity-capture src/capture.js",
     "compile:wasm": "deno task rescript:build && deno task wasm:build",
     "rescript:build": "rescript build",
     "rescript:clean": "rescript clean",
@@ -77,8 +78,8 @@
   ],
   "lint": {
     "include": [
-      "src/**/*.ts",
-      "tests/**/*.ts",
+      "src/**/*.js",
+      "tests/**/*.{ts,js}",
       "benchmarks/**/*.ts"
     ],
     "rules": {
@@ -92,8 +93,8 @@
   },
   "fmt": {
     "include": [
-      "src/**/*.ts",
-      "tests/**/*.ts",
+      "src/**/*.js",
+      "tests/**/*.{ts,js}",
       "benchmarks/**/*.ts"
     ],
     "useTabs": false,