Add full shell, replaceable Omics adapter and bilingual interaction
Implement approved specification #32 and tickets #33-#37. Keep host authentication server-verified and pin session interaction language. Compile scoped base selectors for browser compatibility and retain full gutters during CSS pruning.
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# Native installation CLI
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## Shell configuration
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The schema-v2 `thothii-installation.yaml` accepts this optional section:
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```yaml
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shell:
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mode: full
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defaultLocale: en
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```
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Omitted shell settings resolve to `mode: embedded`, `defaultLocale: en`, and
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`adapter: omics-portal`. Supported modes are `full` and `embedded`. The default
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locale accepts well-formed BCP47 language tags, including tags without a UI catalog
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(for example `fr-CA` or `sr-Latn-RS`). Syntax follows
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[RFC 5646](https://www.rfc-editor.org/rfc/rfc5646.html#section-2.1), including private
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use and grandfathered tags; duplicate variants and extension singletons are rejected.
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The installation preserves the supplied tag; the frontend resolves available
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translations and falls back to English. No catalog or language-registry allowlist
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is imposed by the installer. The only supported adapter is `omics-portal`.
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Invalid values and unknown descriptor fields are rejected. In full mode, a known
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adapter setting is ignored and omitted from the resolved public configuration.
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Shell selection is independent of `profile` and authentication.
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New installations can select these values with `tht setup --shell-mode full
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--shell-default-locale en`. The optional `--shell-adapter omics-portal` selects the
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embedded adapter explicitly. Corresponding environment answers are
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`THT_SETUP_SHELL_MODE`, `THT_SETUP_SHELL_DEFAULT_LOCALE`, and
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`THT_SETUP_SHELL_ADAPTER`; explicit flags take precedence. Omitting all three
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preserves the existing setup descriptor format and uses the defaults at load time.
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Setup does not overwrite an existing descriptor with different settings.
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## Public runtime projection
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The installation generation workflow (`modelprojection.Generate`, used
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by setup, lifecycle operations, and `installation generate`) publishes `generated/frontend/config.js` next
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to the model artifacts, relative to the descriptor directory. It contains only:
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```js
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window.__THOTHII_CONFIG__ = {
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"backendBaseUrl": "/api",
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"shell": {
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"mode": "embedded",
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"defaultLocale": "en",
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"adapter": "omics-portal"
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}
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};
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```
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For full mode, `shell.adapter` is absent. No secret values, model configuration,
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authentication configuration, or host filesystem paths enter this JavaScript.
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The standalone browser API address remains same-origin `/api`; it never uses
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the private nginx upstream `http://core:8787`. The Omics document must continue
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to supply its same-origin `/datamart-builder/api` override when mounting the
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application under that prefix; selecting an adapter does not infer API routing.
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The automatically included `generated/compose.models.yaml` adds a read-only file
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bind from `generated/frontend/config.js` to `/usr/share/nginx/html/config.js` on
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the frontend service. Missing sources fail instead of becoming directories
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(`bind.create_host_path: false`). The frontend receives
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`THT_FRONTEND_CONFIG_REVISION=sha256:<hash-of-config.js-bytes>` so Compose recreates
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it when public settings change. Shell changes do not revise core's model settings.
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Only the public file is mounted into the frontend, not the generated directory.
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Publication retains the existing whole-generation replacement and rollback
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behavior. Identical outputs keep file identities; projection drift checks include
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the public file, Compose definition, and POSIX read permissions. Candidate directories
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are explicitly set to `0755` and files to `0644`, independent of the host umask, so
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nginx and core can read their file mounts under different UIDs. The enclosing private
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installation directory is not made public. Existing permission drift is repaired by
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publishing a new complete generation, using the same rollback path as content changes.
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A running container requires the normal
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Compose lifecycle step to pick up a changed file bind. No image rebuild is needed.
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The generic image retains its empty fallback config, and nginx already serves
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`/config.js` with `no-store, no-cache, must-revalidate`.
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`docker/smoke/frontend-smoke.sh` checks both the generic image fallback and the
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installed public projection. Its optional file argument permits the same check
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against generated output in targeted host tests.
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To generate files before rebuilding or launching containers, use the upgraded CLI:
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```sh
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/usr/local/bin/tht --installation /Users/mp/projects/ThothII/deploy/psd/thothii-installation.yaml installation generate
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```
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This command validates the installation and publishes the common runtime generation.
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It invokes no Docker commands and does not modify the descriptor, authored model
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catalog, environment, or authentication configuration. A shell-only descriptor change
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preserves model projection contents, while the common generation may replace their
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file identities. It is not a shell-only writer: model projections are always derived
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from the current descriptor. Run the existing preview rebuild after this command to
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replace containers with the upgraded images and updated projection mounts.
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