Fix silent loss of files-to-download entries with directory destinations - #402
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…omic The inheritance merge keyed files-to-download entries by the raw dest string, so distinct files sharing a directory-form dest (trailing separator) collapsed into one identity and all but the last entry were silently dropped. The merge identity is now the normalized final file path: a directory-form dest is combined with the source filename, derived by a helper shared with the download-time destination resolution so the two stay in lockstep. The shared helper decodes GitLab API raw-file URLs, so a parent entry resolved to such a URL still matches a child override and deploys under its real filename instead of the literal raw. Duplicate identities within one mcp-servers, skills, or files-to-download list now collapse to the last entry with a warning instead of silently. Entries resolving to the same final path are deduplicated before the parallel download phase, and downloads are written atomically via a temp file and rename so a race or interruption can never leave a partially-written file.
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Summary
files-to-download: the merge identity was the rawdeststring, so distinct files sharing a directory-form dest (trailing/or\) collapsed into one identity and all but the last entry were silently dropped (in a real incident, two of three shared hook libraries were never deployed)._source_filename()helper shared with the download-time destination resolution so the two can never diverge. The helper decodes GitLab API raw-file URLs, so pre-merge source resolution of remote parents no longer breaks identity matching (and such entries now deploy under their real filename instead of the literalraw).mcp-servers,skills, orfiles-to-downloadlist now collapse to the last entry with a warning instead of silently.handle_resourcewrites atomically (temp file +os.replace), so a same-path race or interruption can never leave a partially-written file.docs/environment-configuration-guide.md): key reference, merge-strategies table, and inheritance bullets now state the normalized-final-file-path identity.Test plan
TestFilesToDownloadDirectoryDestMergewith a fixture pair reproducing the incident scenario.uv run pre-commit run --all-filesfully green.