Config::overlay() on pipeline session_options causes "File doesn't exist" on Model load

Describe the bug
Config::overlay() appends pipeline entries instead of merging by model_id, causing "File doesn't exist" error on Model load

When calling Config.overlay() with a JSON that contains a model.decoder.pipeline array,
the overlay appends new pipeline entries instead of merging into existing entries by model_id.
This leaves the pipeline vector with extra entries that have empty filename fields,
causing og.Model(config) to fail with:

To Reproduce
Steps to reproduce the behavior:

Reproduction Steps

1. Load a decoder-pipeline model config (e.g. one with embeddings, context, iterator, lm_head in the pipeline)
2. Apply an overlay that targets pipeline sub-model session_options:

import onnxruntime_genai as og

config = og.Config("C:/path/to/model/")
overlay = '''{
  "model": {
    "decoder": {
      "pipeline": [
        {
          "submodel":  { "session_options": { "enable_profiling": "test" } }
        }
      ]
    }
  }
}'''
config.overlay(overlay)
model = og.Model(config)  # ← RuntimeError here

**Expected behavior**
The overlay should find the existing pipeline entry by model_id ("context", "iterator") and merge/update its fields in-place, consistent with how provider_options overlays work (matched by name).


**Additional context**
I guess the root cause is In src/config.cpp, PipelineModelObject_Element::OnObject() always calls emplace_back() without checking for an existing entry with the same model_id.

Start with the Python reproduction in the issue, then inspect src/config.cpp and PipelineModelObject_Element::OnObject(). Compare its handling of pipeline entries with the provider_options overlay behavior described in the issue. Done means overlaying session_options updates the matching pipeline entry without adding entries with empty filename fields, and og.Model(config) loads successfully.