Add MPNST treated drug-combination experiments

[jjacobson95]

Pipeline Hardening/Debugging PR # 10

Add MPNST treated drug-combination experiments

Adds the experiment-generation half of the MPNST treated update: treated-microtissue drug-combination experiments, plus fixes to how drug data is pulled from Synapse. This is the largest PR in the stack, because most of it is one new script that cannot be meaningfully broken up.

Reviewer note: how to read this efficiently

The heavy file is 03_get_experiments_with_treated.R (1,640 new lines). To review the actual change in logic rather than reading it cold, compare it against the preserved original:

git diff mpnst-treated-experiments -- \
  coderbuild/mpnst/03_get_experiments_orig.R \
  coderbuild/mpnst/03_get_experiments_with_treated.R

03_get_experiments_orig.R is the pre-change script, kept in the tree specifically for this comparison. The most useful areas to focus on are the treated-microtissue (MT) code path and the step that combines treated and untreated results.

New treated-experiment builder (03_get_experiments_with_treated.R)

• Generates the treated microtissue drug-combination experiments.
• Carries verbose, section-by-section logging and guards so that an empty intermediate result prints clear diagnostics instead of crashing the downstream steps. It also has explicit per-section skip switches (MT / PDX / combine) that make it possible to re-run just one part while debugging; all are left enabled by default.

Drug-data source fixes (02_get_drug_data.R)

• Handles a Synapse manifest column that was renamed from PDX_Drug_Data to PDXDrugData in 2025 by checking for either name.
• The values in that column may now be file names rather than Synapse IDs, so it filters to genuine syn######## entries before querying, and skips PDX drug extraction cleanly when the column is absent.

Existing experiment script and packaging

• 03_get_experiments.R: substantial reconciliation so the untreated path stays consistent with the new treated path.
• 03_get_experiments_orig.R: preserved original, kept for the diff described above.
• build_exp.sh / build_drugs.sh: run the treated experiment steps.
• requirements.r: R dependencies for the experiment step.

Scope: 7 files (about 2,648 added lines). Base: mpnst-treated-samples-and-omics. Large by nature: the treated-experiment logic is a single script.

Closes #394