Six fixes in one commit, addressing every Copilot comment except #7
(dead code, deferred to a later cleanup pass).

#4 — manifest shape mismatch (critical):
  push.ts was still reading/writing the old manifest format
  (files[path] = hashString) while pull.ts and sync.ts use the new
  {localHash, remoteMtime} shape. push now uses the new shape,
  migrates old manifests on read (mirrors sync.ts detector), and
  refreshes remoteMtime via getRemoteMtimes() after a successful
  upload so the next pull/sync sees a consistent picture.

#3 — partial-success manifest (important):
  In --batch mode we were marking every instance as synced when
  result.uploaded > 0, even if some failed. Now we derive failed
  paths from result.errors and only add successes to the manifest.
  Failed uploads stay out and get retried on the next run.

#6 — ATOMIC_SOURCE_EXTENSIONS gap (important):
  EXTENSION_MAP was missing .tsx/.jsx/.cjs/.scss/.less/.sass, so
  those extensions got application/octet-stream and were routed
  through individual POST instead of /_atomic despite being listed
  as atomic-source compatible. Now mapped to
  application/typescript/javascript and text/x-* respectively, so
  isTextFile() returns true and they take the atomic path.

#2 — CLI --version out of sync:
  program.version() was hardcoded to '1.0.0' while package.json is
  at 1.0.1. Now reads from package.json via createRequire so
  boxel --version stays accurate on every release.

#1 — --batch-size NaN guard:
  parseInt on bad input (e.g. "abc") returned NaN, which bypasses
  `?? 10` and flows into the uploader as NaN. Now uses a
  parsePositiveInt parser that throws InvalidArgumentError with
  a friendly message on non-positive-integer input.

#5 — invalid-JSON test expectation:
  The test expected data.type='file' but the code (correctly) emits
  'source' because /_atomic only accepts 'card' and 'source'
  resource types. Test updated to match the correct contract.

All 164 tests pass (was 163/164 before this commit).

Co-Authored-By: Claude Opus 4.7 (1M context) <[email protected]>

Six fixes in one commit, addressing every Copilot comment except #7
(dead code, deferred to a later cleanup pass).

#4 — manifest shape mismatch (critical):
  push.ts was still reading/writing the old manifest format
  (files[path] = hashString) while pull.ts and sync.ts use the new
  {localHash, remoteMtime} shape. push now uses the new shape,
  migrates old manifests on read (mirrors sync.ts detector), and
  refreshes remoteMtime via getRemoteMtimes() after a successful
  upload so the next pull/sync sees a consistent picture.

#3 — partial-success manifest (important):
  In --batch mode we were marking every instance as synced when
  result.uploaded > 0, even if some failed. Now we derive failed
  paths from result.errors and only add successes to the manifest.
  Failed uploads stay out and get retried on the next run.

#6 — ATOMIC_SOURCE_EXTENSIONS gap (important):
  EXTENSION_MAP was missing .tsx/.jsx/.cjs/.scss/.less/.sass, so
  those extensions got application/octet-stream and were routed
  through individual POST instead of /_atomic despite being listed
  as atomic-source compatible. Now mapped to
  application/typescript/javascript and text/x-* respectively, so
  isTextFile() returns true and they take the atomic path.

#2 — CLI --version out of sync:
  program.version() was hardcoded to '1.0.0' while package.json is
  at 1.0.1. Now reads from package.json via createRequire so
  boxel --version stays accurate on every release.

#1 — --batch-size NaN guard:
  parseInt on bad input (e.g. "abc") returned NaN, which bypasses
  `?? 10` and flows into the uploader as NaN. Now uses a
  parsePositiveInt parser that throws InvalidArgumentError with
  a friendly message on non-positive-integer input.

#5 — invalid-JSON test expectation:
  The test expected data.type='file' but the code (correctly) emits
  'source' because /_atomic only accepts 'card' and 'source'
  resource types. Test updated to match the correct contract.

All 164 tests pass (was 163/164 before this commit).

Co-Authored-By: Claude Opus 4.7 (1M context) <[email protected]>