ENH: Rework the clang-tidy configuration for C11

[gdevenyi]

The .clang-tidy file has been in the tree since 2025 but nothing has ever
run it, and it shows: two of its entries name clang-analyzer checks that
upstream renamed some releases ago, so --verify-config warned about them.
Run over the whole tree it produced 1697 findings, of which the great
majority came from three style checks. At that ratio nobody reads the
output.

Retuned for what this project actually is: C11, with a shipped ABI.
Measured with clang-tidy 22.1.8, USE_FSL_CODE=ON and USE_CIFTI_CODE=ON,
it now gives 331 findings across 15 checks, every one a defect class:

170 bugprone-macro-parentheses
44 bugprone-unchecked-string-to-number-conversion
25 bugprone-multi-level-implicit-pointer-conversion
19 readability-use-concise-preprocessor-directives
16 bugprone-switch-missing-default-case
13 readability-redundant-casting
5 bugprone-suspicious-string-compare
4 bugprone-suspicious-realloc-usage
3 readability-redundant-control-flow
2 readability-suspicious-call-argument
2 bugprone-misplaced-widening-cast
1 each: readability-implicit-bool-conversion,
readability-function-size, misc-redundant-expression,
bugprone-float-loop-counter

bugprone-macro-parentheses is re-enabled. It had been switched off, but
it is the check that catches the real precedence bugs in the NT_DT_*,
QSTR and NT_FILL macro families.

misc-use-internal-linkage is switched off permanently, with the reason
recorded in the file. It flags 29 functions, 13 of which are symbols
currently exported by libniftiio, libfslio and libcifti. Applying its
fix-it would delete them from the shared libraries. That it looks like a
tidy-up is exactly what makes it dangerous, so the file says so next to
the check rather than leaving the next person to rediscover it.

Every disabled check carries its finding count and the reason, so the
list can be re-argued from evidence instead of taste.

Interface impact: none. On the union of all these changes, configured with USE_FSL_CODE=ON and USE_CIFTI_CODE=ON: all 448 exported symbols across libniftiio, libnifti2, libznz, libfslio, libnifticdf and libcifti are identical to master under nm -D --defined-only, and all ten installed headers are identical under gcc -E -P. Under gcc -dM -E one macro definition differs, intentionally and only in text: #61 makes FSL_RADIOLOGICAL read (-1) so it is safe inside an expression. Its value is still -1, checked by compiling against each installed fslio.h and printing it.

Verification. This branch: builds with gcc 16.1.1, ctest unchanged from master (2 of 345 fail on master itself in this environment; #31 and #29 each fix one). The union of all the PRs: 0 errors under both gcc 16.1.1 and clang 22.1.8, ctest 345/345 under each, and the whole suite under valgrind memcheck with --trace-children=yes gives 484 traced processes with no invalid access, no uninitialised value and no leak in any nifti binary.

Coordination. Every line of every branch was compared, whitespace-normalised, against the diffs of the open PRs (#11, #21, #22, #23, #24). Where one of those already changes a line, the line was left alone, and the few deliberate overlaps are named in the text above. What survives is 17 compiler warnings, all of them on those lines: 9 -Wsign-conversion (5 in fslio.c for #22, 2 in nifti2_io.c and 2 in nifti_tester001.c for #24) and 8 -Wcalloc-transposed-args in nifti_findhdrname and nifti_findimgname, which #11 rewrites. No formatting changes appear anywhere, to stay clear of #10 and #12.

One of a set of independent, single-purpose PRs. Each bases on master and can be merged on its own, in any order.

The full set of PRs (35)

The union of all of them is on the fork as all-changes, if you want to build and test the lot at once.

CI and build

• COMP: Show test output when the starter workflow fails #28 — COMP: Show test output when the starter workflow fails
• COMP: Give install_linking the source directory instead of guessing it #29 — COMP: Give install_linking the source directory instead of guessing it
• COMP: Guard the CMP0169 policy setting so older CMake still configures #30 — COMP: Guard the CMP0169 policy setting so older CMake still configures
• BUG: Compare NIfTI test output by content, not by compressed bytes #31 — BUG: Compare NIfTI test output by content, not by compressed bytes
• COMP: Make the 'Build and Test' analysis workflow run #57 — COMP: Make the 'Build and Test' analysis workflow run

Configuration and documentation

• ENH: Rework the clang-tidy configuration for C11 #32 — ENH: Rework the clang-tidy configuration for C11
• COMP: Add a shared compiler warning set #33 — COMP: Add a shared compiler warning set
• COMP: Enable _FORTIFY_SOURCE in optimized builds #34 — COMP: Enable _FORTIFY_SOURCE in optimised builds
• COMP: Build as ISO C11 with no compiler extensions #38 — COMP: Build as ISO C11 with no compiler extensions
• DOC: Describe the CMake build and how to run the memory checks #58 — DOC: Describe the CMake build and how to run the memory checks
• COMP: Add CI jobs for clang-tidy and for building with -Werror #59 — COMP: Add CI jobs for clang-tidy and for building with -Werror

Defects

• BUG: Fix cdfbin's argument range check, which could never fire #39 — BUG: Fix cdfbin's argument range check, which could never fire
• BUG: Fix an out-of-bounds indirect call in axio_show_mim_summary #40 — BUG: Fix an out-of-bounds indirect call in axio_show_mim_summary
• BUG: Bound the formatted write in znzprintf, and end the va_list on failure #41 — BUG: Bound the formatted write in znzprintf, and end the va_list on failure
• BUG: Report XML read errors instead of treating them as end of input #42 — BUG: Report XML read errors instead of treating them as end of input
• BUG: Stop returning -1 from functions that return size_t #43 — BUG: Stop returning -1 from functions that return size_t
• BUG: Fix the ambiguous-filename path in nifti_findhdrname #54 — BUG: Stop the library calling exit(), and fix the defects beside it
• BUG: Check the allocations whose result is used immediately #55 — BUG: Check the allocations whose result is used immediately
• BUG: Fix cifti_tool's CIFTI extension search, which never advanced #56 — BUG: Fix cifti_tool's CIFTI extension search, which never advanced
• BUG: Free the extension data when nifti_add_extension fails #62 — BUG: Free the extension data when nifti_add_extension fails
• BUG: Free the header on nifti_tool's duplicate-file failure paths #60 — BUG: Free the header on nifti_tool's duplicate-file failure paths
• BUG: Use memcpy instead of casting to over-aligned pointer types #44 — BUG: Use memcpy instead of casting to over-aligned pointer types
• BUG: Stop casting away const in fslio and cifti #45 — BUG: Stop casting away const in fslio and cifti
• BUG: Bound the aux_file copy by sizeof rather than a repeated 24 #46 — BUG: Bound the aux_file copy by sizeof rather than a repeated 24
• ENH: Make the 64-to-32 bit truncations explicit #52 — BUG: Fix 64-to-32 bit truncations, including a real overflow in fslio
• BUG: Fix signed/unsigned comparisons in the nifti tools #51 — BUG: Fix signed/unsigned comparisons in the nifti tools

Warning and check classes

• STYLE: Add the missing newline at end of nifti1_tool.h #35 — STYLE: Add the missing newline at end of nifti1_tool.h
• ENH: Give the cifti tools' gopt internal linkage #36 — ENH: Give the cifti tools' gopt internal linkage
• COMP: Declare the exported functions that no header declares #37 — COMP: Declare the exported functions that no header declares
• BUG: Give i and j a defined value in nifti_mat44_to_orientation #47 — BUG: Give i and j a defined value in nifti_mat44_to_orientation
• ENH: Zero-initialize the matrix locals clang cannot prove are filled #48 — ENH: Zero-initialise the matrix locals clang cannot prove are filled
• BUG: Give the statement macros a do/while(0) body and drop the stray semicolons #49 — BUG: Give the statement macros a do/while(0) body
• ENH: Pass calloc its arguments in the documented order #50 — ENH: Pass calloc its arguments in the documented order
• BUG: Parenthesize macro arguments and replacement lists #61 — BUG: Parenthesise macro arguments and replacement lists
• ENH: Make the implicit sign conversions explicit #53 — ENH: Make the implicit sign conversions explicit

[hjmjohnson]

The commit messages in this range were rewritten to remove trailers that do not belong in permanent history: Co-Authored-By: naming an AI tool, and Claude-Session: URLs that resolve for nobody. Only messages changed — the tree at the tip of master is byte-identical, and author, committer, and dates are preserved.

This PR's commit on the rewritten master:

• 159d11de03 ENH: Rework the clang-tidy configuration for C11

The SHA recorded above by GitHub is from the pre-rewrite history and no longer resolves.