Address PR review comments: remove debug code, fix variable shadowing, improve error handling

[Copilot]

Addresses 26 review comments from PR #61 identifying linting issues, debug code, and code quality improvements.

Core Fixes

Variable shadowing and naming

• Renamed dir → directory in loop to avoid shadowing builtin
• Renamed shank → shank_name in conditional to clarify reuse pattern
• Removed unused assignments: str(win), row["mouse"], row["manipe"], orphaned os.path.abspath() calls

Error handling improvements

• Replaced bare except Exception with specific except (IndexError, KeyError)
• Added None check before speedMask.copy() to prevent AttributeError
• Added explanatory comments to empty except clauses in linearizer and rawdata_parser

Debug artifacts

• Removed print(outputs_sleep) and unused variable assignment
• Removed --dry-run flag from rsync command
• Removed commented --flat_prior flag

Data access fix

# Before: incorrect subscript access
timeStepPred = self.data_helper[epochMask]

# After: correct nested dictionary access  
timeStepPred = self.data_helper.fullBehavior["positionTime"][epochMask]

Review Comments Not Actionable

Several review comments were incorrect:

• get_true_target() call is valid (windowSizeMS has default)
• ValueError in paper_figures.py correctly exits (doesn't continue to unsafe code)
• Return value assignment in global_classes.py already captures both values
• "Unreachable" statements in gui_elements.py are reachable (inside try-except)
• spikeinterface import is used (not unused)

All changes validated with ruff linting and CodeQL security scan (0 alerts).

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