tapps_upgrade overwrites project-specific customizations without merge strategy

[wtthornton]

Problem

tapps_upgrade uses a full-overwrite strategy for all generated files (CLAUDE.md, AGENTS.md, skills, agents, copilot-instructions, rules). Projects that customize these files to reflect their own architecture (e.g., replacing deprecated tool references with native agent catalog routing) lose those changes on every upgrade.

Current Behavior

Running tapps_upgrade after upgrading to v2.3.0:

• Overwrote a trimmed 70-line CLAUDE.md back to the 168-line template
• Reverted deprecation framing in 10 files (skills, agents, copilot-instructions, rules)
• Required manual re-application of all project-specific edits

Expected Behavior

tapps_upgrade should support a merge strategy that preserves project-specific customizations. Options:

1. Marker-based sections — allow <!-- tapps-custom-start --> / <!-- tapps-custom-end --> blocks that survive regeneration
2. Override files — support .tapps-mcp-overrides/ directory with patches applied after template generation
3. Diff-and-prompt — detect custom changes vs template, show diff, ask before overwriting
4. Section-level control — tapps_upgrade config in .tapps-mcp.yaml to skip specific files or sections

Impact

Every project that customizes generated files must re-apply edits after every upgrade. This is the #1 friction point in the upgrade workflow.

Reproduction

1. Run tapps_init in a project
2. Customize CLAUDE.md (e.g., extract TAPPS pipeline to a scoped rules file)
3. Run tapps_upgrade
4. Observe: all customizations are overwritten