chore(cohorter): Move cohorter to apps folder

.agents/skills/add-to-release-please/SKILL.md

@@ -29,7 +29,7 @@ The path is the package key in both config files (repo-relative directory). Conf
 
 | Kind | Path examples |
 |---|---|
-| App | `cogstack-cohorter` |
+| App | `apps/cogstack-cohorter` |
 | Helm chart | `helm-charts/medcat-service-helm` |
 
 Helm charts in this repo are top-level directories under `helm-charts/<chart>/` with a `Chart.yaml`. The package key is that directory. See [Helm charts](#helm-charts) before editing.

.github/workflows/cogstack-cohorter-docker.yml

@@ -6,11 +6,11 @@ on:
     tags:
       - "cohorter-v*.*.*" # e.g., cohorter-v1.2.3
     paths:
-      - "cogstack-cohorter/**"
+      - "apps/cogstack-cohorter/**"
       - ".github/workflows/cogstack-cohorter-docker**"
   pull_request:
     paths:
-      - "cogstack-cohorter/**"
+      - "apps/cogstack-cohorter/**"
       - ".github/workflows/cogstack-cohorter-docker**"
 
 jobs:
@@ -24,13 +24,13 @@ jobs:
       matrix:
         include:
           - name: nl2dsl
-            context: cogstack-cohorter/NL2DSL
-            dockerfile: cogstack-cohorter/NL2DSL/Dockerfile
+            context: apps/cogstack-cohorter/NL2DSL
+            dockerfile: apps/cogstack-cohorter/NL2DSL/Dockerfile
             image: cogstacksystems/cogstack-cohorter-nl2dsl
 
           - name: webapp
-            context: cogstack-cohorter/WebAPP
-            dockerfile: cogstack-cohorter/WebAPP/Dockerfile
+            context: apps/cogstack-cohorter/WebAPP
+            dockerfile: apps/cogstack-cohorter/WebAPP/Dockerfile
             image: cogstacksystems/cogstack-cohorter-webapp
 
     steps:

README.md

@@ -51,7 +51,7 @@ See the latest documentation on [Readthedocs](https://docs.cogstack.org/en/lates
   </tr>
   <tr>
     <td align="center" valign="top" width="50%">
-      <a href="cogstack-cohorter">
+      <a href="apps/cogstack-cohorter">
         <img src="docs/docs/assets/cogstack-logo.png" alt="CogStack Cohorter" height="56"/>
         <br/><strong>CogStack Cohorter</strong>
       </a>

cogstack-cohorter/README.md → apps/cogstack-cohorter/README.md

@@ -27,7 +27,7 @@ A lightweight cohort discovery application that combines:
 - (Optional) GPU setup if you want Ollama GPU acceleration (depends on your host OS)
 
 ### 1) Build and start all services
-From the repo root:
+From this directory:
 
 ```bash
 docker compose up --build

cogstack-cohorter/WebAPP/README.md → apps/cogstack-cohorter/WebAPP/README.md

@@ -8,7 +8,7 @@ This webapp is a cohort app for users to obtain the number of patients satifying
 
 Other runtime dependencies include [ECharts](https://echarts.apache.org/en/index.html) for charts and [popper.js](https://popper.js.org/) for tooltips.
 
-A GitHub Packages token with `read:packages` scope is required to install `@cogstack/frontend-common-react`. Set it in a `.env` file at the `cogstack-cohorter/` root (see `.env.example`) or export it in your shell:
+A GitHub Packages token with `read:packages` scope is required to install `@cogstack/frontend-common-react`. Set it in a `.env` file at the `apps/cogstack-cohorter/` root (see `.env.example`) or export it in your shell:
 
 ```bash
 export NPM_TOKEN=ghp_your_token_here
@@ -44,7 +44,7 @@ There is a script `gen_random_data.js` in `server/data/` folder to generate the
 
 Please make sure to have the six data files ready in the `server/data/` folder before starting the server. To start the server, in the app folder run `cd server && npm install && npm run start`. 
 
-The recommended way to run the full stack (webapp + NL2DSL + MedCAT + Ollama) is via `docker-compose` from the `cogstack-cohorter/` root — see the root-level README and `.env.example` for details. The `NPM_TOKEN` is passed as a BuildKit secret; set it in the `.env` file before building.
+The recommended way to run the full stack (webapp + NL2DSL + MedCAT + Ollama) is via `docker-compose` from the `apps/cogstack-cohorter/` root — see the root-level README and `.env.example` for details. The `NPM_TOKEN` is passed as a BuildKit secret; set it in the `.env` file before building.
 
 ### Environment variables
 
@@ -92,7 +92,7 @@ In Kubernetes these are set as env vars on the webapp container (via helm `cogst
 
 ### Run using Docker with random data
 
-Set `RANDOM_DATA=true` in your `.env` file (or leave it unset — it defaults to `true`), then from the `cogstack-cohorter/` root:
+Set `RANDOM_DATA=true` in your `.env` file (or leave it unset — it defaults to `true`), then from the `apps/cogstack-cohorter/` root:
 
 ```bash
 docker compose up --build

cogstack-cohorter/WebAPP/client-react/README.md → apps/cogstack-cohorter/WebAPP/client-react/README.md

@@ -21,7 +21,7 @@ It keeps the existing Alpine-style template/data model behaviour, while using Re
 
 ## Environment variables
 
-A single `.env` file at the **`cogstack-cohorter/` root** (one level up from `WebAPP/`) is shared between Vite and `docker-compose`. Copy `.env.example` there and fill in values:
+A single `.env` file at the **`apps/cogstack-cohorter/` root** (one level up from `WebAPP/`) is shared between Vite and `docker-compose`. Copy `.env.example` there and fill in values:
 
 ```bash
 cp ../../.env.example ../../.env

cogstack-cohorter/WebAPP/client-react/vite.config.js → apps/cogstack-cohorter/WebAPP/client-react/vite.config.js

@@ -4,7 +4,7 @@ import react from '@vitejs/plugin-react';
 // Express server port (same origin in production; proxied in dev)
 const API_ORIGIN = 'http://localhost:3000';
 
-// Point Vite at the cogstack-cohorter/ root so that it reads the same .env
+// Point Vite at the apps/cogstack-cohorter/ root so that it reads the same .env
 // as docker-compose, eliminating the need for a separate client-react/.env.
 // Both `npm run dev` (Vite) and `docker-compose build` resolve vars from one file.
 const ENV_DIR = '../../';