docs: replace legacy backend docs with clearer guides

Author: Nicolass67

.gitignore

@@ -20,4 +20,4 @@ build/
 /chem_spectra/tmp/
 !/chem_spectra/tmp/.keep
 
-src/
+/src/

README.md

@@ -11,8 +11,12 @@ The frontend is provided by [chem-spectra-client](https://github.com/ComPlat/che
 ## Documentation
 
 1. [Installation](INSTALL.md)
-2. [Demo & step-by-step manual](https://github.com/ComPlat/react-spectra-editor/blob/master/DEMO_MANUAL.md)
-3. Software's [Archicture](./docs/ARCHITECTURE.md)
+2. [Developer onboarding](docs/onboarding.md)
+3. [Backend architecture](docs/architecture.md)
+4. [API reference](docs/api-reference.md)
+5. [Core runtime flows](docs/core-flows.md)
+6. [Diagram maintenance](docs/dev/diagrams.md)
+7. [Demo & step-by-step manual](https://github.com/ComPlat/react-spectra-editor/blob/master/DEMO_MANUAL.md)
 
 ### Run test
 

docs/ARCHITECTURE.md

@@ -0,0 +1,45 @@
+# API Reference
+
+This document lists the HTTP routes exposed by `chem-spectra-app`.
+
+Use `docs/architecture.md` for component boundaries and `docs/core-flows.md` for runtime behavior. This file is the compact route-level reference for handlers, main inputs, and main outputs.
+
+## `file_api`
+
+| Route | Handler | Main input | Main output |
+|---|---|---|---|
+| `POST /api/v1/chemspectra/file/convert` | `chemspectra_file_convert()` | `file`, optional `molfile`, form params | JSON with base64 `jcamp` and `img`, or BagIt `list_jcamps` |
+| `POST /api/v1/chemspectra/file/save` | `chemspectra_file_save()` | `src`, `dst` or `dst_list`, optional `molfile`, form params | `spectrum.zip` containing source, generated files, predictions, optional CSV |
+| `POST /api/v1/chemspectra/file/refresh` | `chemspectra_file_refresh()` | `dst` or `dst_list`, optional `molfile`, form params | JSON with base64 `jcamp` and `img`, or `spectrum.zip` for multiple files |
+| `POST /api/v1/chemspectra/molfile/convert` | `chemspectra_molfile_convert()` | `molfile` | JSON with `smi`, `mass`, and molecule `svg` |
+
+## `transform_api`
+
+| Route | Handler | Main input | Main output |
+|---|---|---|---|
+| `POST /zip_jcamp_n_img` | `zip_jcamp_n_img()` | `file`, optional `molfile`, form params | `spectrum.zip` with JCAMP/image/optional CSV, plus `X-Extra-Info-JSON` |
+| `POST /zip_jcamp` | `zip_jcamp()` | `file`, optional `molfile`, form params | `spectrum.zip` with JCAMP files |
+| `POST /zip_image` | `zip_image()` | `file`, optional `molfile`, form params | `spectrum.zip` with image files |
+| `POST /jcamp` | `jcamp()` | `file`, optional `molfile`, form params | `spectrum.jdx` |
+| `POST /image` | `image()` | `file`, optional `molfile`, form params | `spectrum.png` |
+| `POST /nmrium` | `nmrium()` | NMRium `file` | `spectrum.jdx`, or `404` if conversion fails |
+| `POST /combine_images` | `combine_images()` | `files[]`, form params, optional `extras` | `spectrum.zip` with combined image output |
+
+## `inference_api`
+
+| Route | Handler | Main input | Main output |
+|---|---|---|---|
+| `POST /predict/by_peaks_json` | `chemspectra_predict_by_peaks_json()` | JSON `layout`, `peaks`, `shift`, `molfile` | prediction JSON |
+| `POST /api/v1/chemspectra/predict/nmr_peaks_json` | `chemspectra_predict_by_peaks_json()` | JSON `layout`, `peaks`, `shift`, `molfile` | prediction JSON |
+| `POST /predict/by_peaks_form` | `chemspectra_predict_by_peaks_form()` | form `layout`, `peaks`, `shift`, `molfile`, optional `spectrum` | prediction JSON |
+| `POST /api/v1/chemspectra/predict/nmr_peaks_form` | `chemspectra_predict_by_peaks_form()` | form `layout`, `peaks`, `shift`, `molfile`, optional `spectrum` | prediction JSON |
+| `POST /predict/infrared` | `chemspectra_predict_infrared()` | `layout`, `spectrum`, `molfile` | prediction JSON |
+| `POST /api/v1/chemspectra/predict/infrared` | `chemspectra_predict_infrared()` | `layout`, `spectrum`, `molfile` | prediction JSON |
+| `POST /predict/ms` | `chemspectra_predict_ms()` | `layout`, `spectrum`, `molfile` | prediction JSON |
+| `POST /api/v1/chemspectra/predict/ms` | `chemspectra_predict_ms()` | `layout`, `spectrum`, `molfile` | prediction JSON |
+
+## `spectra_layout_api`
+
+| Route | Handler | Main input | Main output |
+|---|---|---|---|
+| `GET /api/v1/chemspectra/spectra_layouts` | `get_spectra_layouts()` | none | JSON layout mapping from JCAMP data type configuration |