chore: replace prepare script with prepublishOnly across workspace packages

[bshaffer]

• Replace prepare with prepublishOnly across all workspace packages and generator templates so pnpm install does not trigger 280+ uncached builds (reducing install time from 6+ min to ~13s).
• Update pretest in nodejs-proto-files, logging-utils, and tools where prepare was explicitly invoked.

[gemini-code-assist]

Code Review

This pull request updates numerous package.json files across the repository, replacing the 'prepare' script with 'prepublishOnly' to ensure compilation occurs specifically before publishing. The review feedback highlights two opportunities to eliminate redundant steps: first, in 'core/packages/nodejs-proto-files/package.json', where the 'pretest' script performs a duplicate compilation; and second, in 'handwritten/spanner/package.json', where the 'prepublishOnly' script includes an unnecessary manual copy step that is already handled by the 'compile' script.