refactor(tools): remove partial read support from read-file

[cniska]

Summary

• remove start/end line range params from read-file tool, always read full files
• rename readSnippet/readSnippets to readFileContent/readFileContents
• replace silent output truncation with 2000-line hard limit (80k char budget)
• fix tool cache populateSubEntries to handle structured result objects
• simplify file-churn guard to track paths only, no range signatures
• allow re-reading edited files once for follow-up edits (fixes guard deadlock)
• block lifecycle-managed commands (lint/format/verify) via run-command in work mode
• add preamble instruction to run only changed test files, not full suite
• fix /clear and /new duplicate header key warning in TUI
• remove dead code: toInt, formatReadDetail, normalizeReadEntries, range types