Composite and Stitched images do not preserve the Root of the original image files

[EtalumaSupport]

While the Protocol images have the format root_A1_Green_TA1_4xOly the composited and stitched result file names drop the Root.

[ericweiner]

Fix shipped -- ready for bench verification

Root cause: Per-image protocol saves use protocol.capture_root() as a filename prefix (modules/protocol_image_writer.py:266-273). The five post-processors (composite, stitcher, zprojector, video_builder, stack_builder) all dropped that prefix -- four read a DataFrame column "Custom Root" that is never written anywhere in the codebase, and stack_builder had no prefix at all. Result: post-processed outputs collapsed to step-name only, losing the experiment Root the user set.

Fix: modules/protocol_post_processor.py::load_folder now extracts protocol.capture_root() and threads it through kwargs. Each of the five _generate_filename overrides reads kwargs["capture_root"] instead of the dormant column. Broadened during the fix: stack_builder.py:62-82 had the same symptom (no prefix) with a different shape; added to the cluster.

SHA: 4b972e9 on 4.0.0-beta (current tip 4b972e9, 4.0.0-beta14 build).

Regression test: tests/test_issue_501_post_processor_capture_root.py (AST lock on base threading kwarg + per-subclass capture_root read).

Retest signal:

1. Run a protocol with the Capture Root field set to e.g. mytest. Confirm per-image saves are mytest_<step>_<color>_..._.tiff (already worked).
2. Use Image Processing tools to produce a Composite -- expected: mytest_<step>_Composite_<...>.tiff.
3. Use Image Processing tools to produce a Stitched output -- expected: mytest_<step>_<color>_..._stitched.tiff.
4. Use Z-projection / Video / Stack builders -- expected: each output filename starts with mytest_.
5. Pre-fix all four collapsed to step-name only with no mytest_ prefix.

EtalumaSupport, please download the latest beta build and verify the fix. Then either close this issue if fully resolved, or add a note describing what is still happening.

[EtalumaSupport]

Comps, tiles, z-stacks all conserve the root now. I may not have noticed this before but it does include one of the chgannel names in the composite file name. Here it keeps Green in a Green and Red composite.