feat(diagnostics): report a byte entropy profile for one local file (#2331)

* feat(diagnostics): report a byte entropy profile for one local file

The diff adds the MCP tool inspect_byte_entropy and the CLI command
inspect-byte-entropy, both implemented by ByteEntropyService. One
absolute regular file is read offline into observed Evidence: file-wide
SHA-256 and Shannon entropy, then fixed blocks and adjacent runs for an
optional window, using a power-of-two block size from 256 to 65536
(default 4096), with high at 7.2 or above and low at 1.0 or below. A
window past EOF, a missing path, or a non-file is an input error; a size
or identity change during the read is an artifact-changed error; empty
input reports entropy 0; cancellation is honored before and during the
read. Summary detail retains the complete series and returns file
entropy, counts, and the ten longest runs for inspect_analysis_view,
while the registered effect remains read-only Evidence and the
diagnostics docs record the operation and its errors.

* fix(diagnostics): flag zero-size files as not shown empty

Generated files such as Linux /proc entries report size 0 while holding
content, so inspect_byte_entropy read nothing and returned an empty-looking
report. A file that reports size 0 now carries a limitation that the result
does not show the file is empty. The result stays a success because the
tool reads the declared size, which the file-stability checks depend on.

* fix(mcp): reject unsupported diagnostic summaries before inspection

* fix(ci): repair integrated checks and Hopper test baseline

* test(entropy): use shared MCP schema verification after merge

* fix(catalog): list inspect_byte_entropy under its own provider

Adding inspect_byte_entropy to BINARY_DIAGNOSTICS_TOOL_CONTRACTS put it
under pwntools-elf in the generated product catalog, because the
pwntools group took every binary diagnostics tool except
inspect_pe_resources. The service reports provider byte-entropy.

Add a BYTE_ENTROPY_PROVIDER identity beside PE_RESOURCES_PROVIDER, use
it in ByteEntropyService, give it its own catalog group, and name the
pwntools tools (inspect_binary_layout, inspect_recorded_crash)
explicitly so a new diagnostics tool is not attributed to pwntools by
default. The catalog test pins both groups.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01KFTE4BHbGYzgf8Uhzcppdh

* fix(cli): resolve the byte-entropy path with absoluteCallerPath

main replaced the node:path resolve import in binaryDiagnosticsCommands.ts
with absoluteCallerPath (#4067), so the byte-entropy command's
resolve(args.path) no longer type-checks once the PR is merged with main.
Use absoluteCallerPath like the other commands, and add
src/filesystem/callerPath.ts matching main so the branch builds on its own.

* fix(diagnostics): retain entropy read cleanup ownership

* docs(diagnostics): explain entropy output capacity

* fix(diagnostics): preserve entropy cancellation outcomes

* fix(diagnostics): close the entropy input and warn on large reports

Public inspect_byte_entropy input now uses publicInputStrictObject before
detail is added, so unknown keys stay rejected on the advertised schema.
The tool description warns that complete output can become very large and
points callers to a shorter length or a larger block_size.

Co-authored-by: morluto <morluto@users.noreply.github.com>

* fix(diagnostics): keep byte-entropy registration mergeable with main

Register inspect_byte_entropy beside layout inspection and reject
unretained summaries before the file read, without editing workflows.

Co-authored-by: morluto <morluto@users.noreply.github.com>

* fix(diagnostics): register byte entropy with the shared tool options

Use toolRegistrationOptions so the handler typechecks on this branch and
on main, and still refuse unretained summaries before the file read.

Co-authored-by: morluto <morluto@users.noreply.github.com>

---------

Co-authored-by: Matt Van Horn <455140+mvanhorn@users.noreply.github.com>
Co-authored-by: morluto <76467478+morluto@users.noreply.github.com>
Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
Co-authored-by: Kaoru0822 <208281322+kaoru0822-kitauji@users.noreply.github.com>
Co-authored-by: Cursor Agent <cursoragent@cursor.com>
Co-authored-by: morluto <morluto@users.noreply.github.com>

docs/user-visible-errors.csv

@@ -116,3 +116,5 @@ Then rerun this installer.",implemented,verified by shell branch inspection
 90,install.sh:version mismatch,Installed rea reports a different version,installed version ACTUAL does not match EXPECTED.,Low risk; gives exact integrity mismatch,Keep current copy,unchanged,verified by exact installer test
 90.5,@modelcontextprotocol/server:tool input validation,Caller sends arguments that violate a declared tool schema,"Canonical invalid_request with the SDK diagnostic plus recovery.kind=inspect_input_contract and a bounded instruction to read the advertised schema or call tools/list",Keeps field/type correction while telling the agent how to recover; diagnostics over 4 KiB stay on the existing retained-error path,Normalize ordinary validation failures and retain oversized diagnostics,verified by real in-memory and stdio MCP client/server calls with wrong argument types
 90.6,incur:unknown CLI command,Caller enters an unknown REA command,"'COMMAND' is not a command for 'rea'. Suggested command: rea --help",Low risk; identifies input and exact discovery action,Keep framework-generated copy,unchanged,verified by real packaged dispatcher invocation
+91,src/application/binaryDiagnostics/ByteEntropyService.ts,Invalid file or window,"Expected a regular file.; Selected file could not be found.; Selected byte window extends beyond the end of the file.; File size exceeds exact numeric offset representation.",Invalid selection cannot produce complete entropy Evidence,Choose a readable regular file and a window within its byte size,implemented,entropy service and MCP boundary tests
+92,src/domain/analysisView/byteEntropyView.ts,Non-summary entropy view,Byte entropy Evidence supports the summary view; retrieve parent Evidence for the complete block series.,Unsupported view selection,Use the summary view or retrieve complete parent Evidence,implemented,typed input rejection