feat: Add Spectronaut pivot report import with condition setup, inline exp design, and gene symbol splitting

[cliandouble08]

Summary

• Adds Spectronaut pivot report (TSV) import with per-file condition setup: upload a Spectronaut-exported condition setup TSV to auto-populate run labels, conditions, and replicates
• Detects available quantification suffixes (e.g. .PG.Quantity, .PG.IBAQ) from pivot report columns and lets the user select which metric to keep
• Adds optional identifier splitting: extract first ID from semicolon-delimited protein group columns for CSV/Excel uploads
• Adds optional gene symbol splitting for GCT uploads — now a user-controlled checkbox with configurable separator
• Supplements the file-upload experimental design step with an inline rhandsontable editor for CSV/Excel workflows
• Supports sample_annotation column in experimental design to rename sample columns to friendly names; renames are applied at process time and live-previewed as the user types
• Live-updates the data preview panel when the user toggles identifier splitting, imports a condition setup file, changes the quantification suffix, or edits sample annotation names in the exp design table
• Preserves the full rename chain (raw run label → Spectronaut condition name → sample annotation name) in cdesc$original_column_name; exports a GCT_originalColNames file whenever any column renaming occurred
• Adds protigy.enable_spectronaut R option in app.R to gate the Spectronaut condition setup UI — set FALSE for public releases without Spectronaut-specific UI, TRUE for internal use

Changes

New files:

• R/sidebar_setup_helpers_spectronaut.R — Spectronaut parsing, column detection, condition setup reading, and preprocessing helpers (read_spectronaut_condition_setup, detect_quant_suffixes, apply_spectronaut_condition_setup, buildExpDesignFromConditionSetup)
• tests/testthat/test-spectronaut-processing.R — unit tests for Spectronaut helpers

Modified files:

• R/sidebar_setup.R — Spectronaut upload path, inline exp design flow, identifier splitting wiring; live preview observers for split identifier, condition setup import, and sample annotation edits; fix rhandsontable crash by setting contextMenu directly on widget object; fix protigy_id propagation through identifier selection and exp design steps; show all columns (including protigy_id) in exp design table; apply sample annotation renames at process time and build original_cid_map from the full rename chain
• R/sidebar_setup_helpers_csv-excel-processing.R — extract_protigy_id, classifyColumns updates for rhandsontable integration; per-file condition setup and ID splitting UI; createCdesc accepts original_cid_map and writes cdesc$original_column_name; Spectronaut condition setup UI gated by protigy.enable_spectronaut option
• R/sidebar_setup_helpers_experimental-design.R — inline editable exp design support
• R/sidebar_setup_helpers_shiny.R — gctSetupUI gains gene symbol split checkbox + separator input
• R/sidebar_setup_helpers_GCT-processing.R — wiring updates
• R/tab_summary.R — accepts column_rename_map reactive; GCT_original_originalColNames_export_function handles both Spectronaut and sample annotation rename sources, adds renamed_column_name to cdesc for traceability
• R/app_ui.R — exp design panel and data preview panel in sidebar
• app.R — protigy.enable_spectronaut feature flag (default FALSE)
• inst/setup_parameters/setupDefaults.yaml — new default parameters
• inst/custom.css — word-wrap fix for long label inputs

Dependencies added: rhandsontable

Bug fixes

• rhandsontable crash (Error in &&: invalid 'y' type in 'x && y'): contextMenu = list(...) passed via ... to hot_table() which runs if (!is.null(contextMenu) && contextMenu) — fails for list type. Fixed by setting ht$x$contextMenu directly after widget creation.
• protigy_id not visible in downstream steps: preview was never updated after label submission. Fixed by updating preview after storing the pristine copy.
• CID not updated from sample_annotation: rename was only applied in the condition file upload observer, not at "Process Files" time. Fixed by applying at process time.
• Original raw column names lost: tracked via raw_column_names_per_label and composed into original_cid_map at process time.

Test plan

• Upload a Spectronaut pivot report CSV — verify preprocessing step appears with run labels and suffix selector
• Upload a Spectronaut condition setup TSV — verify it live-updates the data preview with renamed column headers
• Select a quantification suffix and confirm only matched columns are kept and renamed
• Toggle "Split identifier column" — verify data preview immediately shows protigy_id as first column; uncheck to revert
• Upload a standard CSV/Excel file — confirm inline rhandsontable exp design editor works without crashing
• Edit sample_annotation column in exp design table — verify data preview updates live with new column names
• Enable gene symbol splitting on a GCT upload — verify separator is respected
• Process files and verify all columns (including protigy_id) appear in the exp design table
• Verify devtools::test() passes including new spectronaut and CSV/Excel tests
• Run devtools::check() with no new errors/warnings
• Set options(protigy.enable_spectronaut = FALSE) and confirm Spectronaut checkbox is hidden; set TRUE to re-enable

Closes #56