refactor(json): model JsonFile encode/write options as a typed struct

Replace the i64 bitmask + encode_with_indent split with a JsonEncodeOptions
struct (Default = JSON_UNESCAPED_SLASHES|JSON_PRETTY_PRINT|JSON_UNESCAPED_UNICODE,
default indent). encode/write each get a default form plus an explicit
encode_with_options/write_with_options variant, mirroring PHP's optional
$options argument. write_with_options always encodes with self.indent, matching
PHP write().

Also reconcile call sites with the PHP sources: most ported sites passed 0 where
Composer omits the argument (= default flags), so JsonManipulator/ShowCommand and
JsonConfigSource now use the default options; only ComposerRepository and Locker
genuinely pass 0.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

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