#15613: fix(config): align default pipelines across loadConfig and readConfigFileSnapshot

## Summary Three code paths in `src/config/io.ts` apply different subsets of defaults: | Default function | loadConfig | snapshot (file exists) | snapshot (no file) | |---|---|---|---| | applyCompactionDefaults | Yes | **No** | Yes | | applyContextPruningDefaults | Yes | **No** | Yes | | applyLoggingDefaults | Yes | Yes | **No** | This causes the config editor UI to compute incorrect diffs. ## Fix - Add missing `applyCompactionDefaults` and `applyContextPruningDefaults` to the snapshot file-exists path - Add missing `applyLoggingDefaults` to the snapshot no-file path ## Test plan - [x] Existing config IO tests pass <!-- greptile_comment --> <h2>Greptile Overview</h2> <h3>Greptile Summary</h3> Updates `src/config/io.ts` so `readConfigFileSnapshot()` applies the same runtime default pipeline regardless of whether a config file exists (adds `applyCompactionDefaults`/`applyContextPruningDefaults` on the file-exists path, and adds `applyLoggingDefaults` on the no-file path). This aligns snapshot behavior with `loadConfig()`, reducing UI diffs caused by inconsistent default application. Main behavior change is limited to which defaults are applied in the snapshot config object; parsing/validation/include resolution remains unchanged. <h3>Confidence Score: 4/5</h3> - This PR is likely safe to merge, with one behavioral concern around mutation/aliasing in the snapshot pipeline to double-check. - Changes are narrowly scoped to applying missing default functions in `readConfigFileSnapshot`, matching existing `loadConfig` behavior. The main risk is that snapshot objects are mutated in-place via `normalizeConfigPaths`, which can create reference aliasing if other steps reuse object graphs, potentially impacting diff/patch computation. - src/config/io.ts _{Last reviewed commit: d604095} <!-- greptile_other_comments_section --> <!-- /greptile_comment -->