Delete shell scripts and update Dockerfile entrypoint

## Parent PRD

#1670

## What to build

With all shell script logic now in TypeScript (#1671, #1672, #1673, #1674), delete the shell scripts and wire everything together.

Delete:
- `docker-entrypoint.sh`
- `process-environment.sh`
- `setup-ssl.sh`
- `packages/graph-explorer-proxy-server/docker-startup.sh` (dead code, uses pm2)

Dockerfile changes:
- Change ENTRYPOINT from `["./docker-entrypoint.sh"]` to `["node", "packages/graph-explorer-proxy-server/dist/node-server.js"]`
- Remove `RUN chmod +x` lines for shell scripts
- Keep openssl in the image (needed for cert generation)
- Keep the `NEPTUNE_NOTEBOOK` ARG → ENV propagation (build-time path selection)

Server startup changes:
- Update `node-server.ts` to call the startup-config pipeline (#1673) before creating the Express app
- Call SSL cert generation (#1672) when HTTPS is enabled
- Pass resolved config to `createApp()` and `startServer()`

Documentation:
- Update `docs/development.md` references to shell scripts
- Update `docs/references/default-connection.md` if needed

## Acceptance criteria

- [ ] All four shell scripts deleted
- [ ] Dockerfile ENTRYPOINT is `["node", "packages/graph-explorer-proxy-server/dist/node-server.js"]`
- [ ] `node-server.ts` runs config pipeline → SSL setup → Express app creation
- [ ] Docker image builds and starts successfully (standard mode)
- [ ] Docker image builds and starts successfully (Neptune Notebook mode with `--build-arg NEPTUNE_NOTEBOOK=true`)
- [ ] Existing CI workflows pass without changes (both Docker build variants)
- [ ] Documentation updated

## Blocked by

- Blocked by #1673
- Blocked by #1674
- Blocked by #1672

## User stories addressed

- User story 9
- User story 11
- User story 12

Start with packages/graph-explorer-proxy-server/node-server.ts, the Dockerfile, and the four listed shell scripts; review blocked issues #1672, #1673, and #1674 first. Verify the startup-config pipeline, SSL setup, app creation, and server start are connected, then run both standard and NEPTUNE_NOTEBOOK Docker builds and check the documentation references.

Written by the indexing model from the issue text.