MultiSEMTileRemovalClient implementations

[trautmane]

These changes support pipeline removal of problem z-layers and z-layer-MFOVs from multi-SEM stacks. I plan to use this process instead of the FIBSEM tile patching process because tiles move around too much between multi-SEM z-layers.

I have a few more changes to make. When those are done, I plan to assign @minnerbe as a reviewer.

[Copilot]

Pull request overview

Adds a new multi-SEM tile/layer removal capability that can be run either as a standalone Java client or as an alignment-pipeline step, enabling in-place removal of entire scans (z-layers) and/or specific MFOVs from multi-SEM stacks (optionally collapsing remaining z values).

Changes:

• Introduces MultiSEMTileRemovalClient implementations (Java and Spark/pipeline-step wrapper) plus new parameter types to describe per-stack removal operations.
• Adds a Render web-service client endpoint helper to fetch tile IDs for a specific z (GET .../tileIds?minZ=...&maxZ=...) used by the removal logic.
• Extends pipeline configuration to include a tileRemovalList and a new pipeline step ID (REMOVE_TILES).

Reviewed changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
render-ws-with-mongo-db/other/load-rough-align-data.sh	Removes an older rough-align helper script (no longer maintained in this PR).
render-ws-spark-client/src/main/java/org/janelia/render/client/spark/pipeline/AlignmentPipelineStepId.java	Adds REMOVE_TILES pipeline step ID wired to the Spark removal client.
render-ws-spark-client/src/main/java/org/janelia/render/client/spark/pipeline/AlignmentPipelineParameters.java	Adds tileRemovalList to pipeline parameters and exposes a getter.
render-ws-spark-client/src/main/java/org/janelia/render/client/spark/multisem/MultiSEMTileRemovalClient.java	New pipeline step / driver-only Spark wrapper that calls the Java removal client per stack.
render-ws-java-client/src/main/java/org/janelia/render/client/RenderDataClient.java	Adds getTileIdsForZ() REST helper needed for MFOV/layer identification and removal.
render-ws-java-client/src/main/java/org/janelia/render/client/parameter/StackWithRemovalParameters.java	New parameter object pairing a StackId with removal parameters (for pipelines / multi-stack runs).
render-ws-java-client/src/main/java/org/janelia/render/client/parameter/MultiSEMTileRemovalParameters.java	New CLI/JSON parameters describing scan and scan+MFOV removals plus optional stack collapsing.
render-ws-java-client/src/main/java/org/janelia/render/client/multisem/MultiSEMTileRemovalClient.java	New core implementation: validates targets, performs in-place deletions, optional z-collapse, then completes the stack.
render-app/src/test/java/org/janelia/alignment/multisem/MultiSemUtilitiesTest.java	Extends parsing tests to include scan-string extraction.
render-app/src/main/java/org/janelia/alignment/multisem/MultiSemUtilities.java	Adds getScanStringForTileId() used to map scan names to z-layers idempotently.

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[minnerbe]

Looks good to me. Thanks, @trautmane!