fix: apply init-script renames in a single pass per file

[beeman]

Why

Replacing one search term at a time re-scanned the output of earlier substitutions, so a project name containing a template term compounded on every pass: naming a counter-template project mycountergill produced mymymycountergillgillgill in program names, file names, and the IDL path the setup script then failed to resolve. The same compounding existed across calls — the package.json project rename, each rename entry, and template option renames each walked overlapping trees in sequence, so even a single-pass replacement per call would still re-scan what a previous call wrote.

What

• searchAndReplace combines all substitutions into one alternation regex (longest match first) and applies them in a single pass over each file's contents and name, so no replacement output is ever re-matched
• New searchAndReplaceScopes applies multiple rename sources together: substitutions are unioned per file, with the narrowest scope winning on conflicting terms
• initScriptRename collects the project rename and all rename entries as scopes and applies them in one call
• initScriptOptions returns its rename scopes instead of applying them, and initScriptRename folds them into the same pass after the entry scopes
• An unreadable scope root logs and continues instead of aborting the remaining scopes, and dry runs no longer recurse into directories under the paths they only pretended to rename
• New file-system-level test suite (test/init-script-rename-files.test.ts) reproduces the issue scenario end to end, plus unit tests for compounding, duplicated substitutions, scope precedence, and error isolation

Notes

Verified against the real CLI with live templates using hostile names (my-scaffold-counter on kit/nextjs, counter-scaffold on web3js/web3js-next-tailwind-counter) — no doubling in either. Two known issues are intentionally out of scope: a single lowercase rename term still maps to its kebab form in Rust contexts (pub mod my-counter), and the project-wide rename rewrites the template's own README install command; both predate this change.

Fixes #192, fixes #193

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Latest commit: 60f0db9

The changes in this PR will be included in the next version bump.

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create-solana-dapp	Patch

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commit: 60f0db9

[greptile-apps]

Greptile Summary

This PR applies project, template-entry, and option renames together in one pass per file, preventing replacement output from being processed again.

• Adds scope-aware substitutions with narrow-scope precedence.
• Preserves explicitly targeted paths beneath normally excluded directories.
• Updates init-script orchestration to collect option rename scopes before applying renames.
• Adds filesystem and unit coverage for compounding, scope precedence, dry runs, and isolated scope errors.

Confidence Score: 5/5

The PR appears safe to merge.

No blocking failure remains; the previously reported excluded-directory regression is fixed, and the earlier commit-signature report was already established as invalid for an SSH-signed commit verified by GitHub.

Important Files Changed

Filename	Overview
src/utils/search-and-replace.ts	Introduces single-pass, scope-aware replacement and correctly retains explicit scopes beneath excluded directories.
src/utils/init-script-rename.ts	Collects project, entry, and option rename scopes and applies them in one combined pass.
src/utils/init-script-options.ts	Returns option instructions and deferred rename scopes for combined processing.
src/utils/create-app-task-run-init-script.ts	Passes collected option scopes into the unified init-script rename operation.
test/search-and-replace.test.ts	Covers single-pass substitutions, precedence, excluded-path targeting, and per-scope error isolation.
test/init-script-rename-files.test.ts	Adds filesystem-level regression coverage for project names containing template rename terms.

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